PDB Short entry for 1PH7 HEADER DNA BINDING PROTEIN/DNA 29-MAY-03 1PH7 TITLE CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN TITLE 2 COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGIGG COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*T)-3'; COMPND 3 CHAIN: G, H; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CHAINS G AND H ARE A G-QUARTET LINKED DNA DIMER, 3' COMPND 6 TERMINAL SINGLE STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES.; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*IP*GP*G)-3'; COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES; COMPND 12 OTHER_DETAILS: CHAIN D IS SINGLE STRAND DNA, 3' TERMINAL SINGLE COMPND 13 STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES, G TO I SUBSTITUTION.; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: TELOMERE-BINDING PROTEIN ALPHA SUBUNIT; COMPND 16 CHAIN: A; COMPND 17 SYNONYM: TELOMERE-BINDING PROTEIN 56 KDA SUBUNIT, TEBP ALPHA; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: ALANINE VERSION; COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: TELOMERE-BINDING PROTEIN BETA SUBUNIT; COMPND 22 CHAIN: B; COMPND 23 FRAGMENT: RESIDUES 9-224; COMPND 24 SYNONYM: TELOMERE-BINDING PROTEIN 41 KDA SUBUNIT, TEBP BETA; COMPND 25 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHESIZED; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: STERKIELLA NOVA; SOURCE 9 ORGANISM_TAXID: 200597; SOURCE 10 GENE: MAC-56A AND MAC-56K AND MAC-56S; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PKKT7; SOURCE 16 MOL_ID: 4; SOURCE 17 ORGANISM_SCIENTIFIC: STERKIELLA NOVA; SOURCE 18 ORGANISM_TAXID: 200597; SOURCE 19 GENE: MAC-41A AND MAC-41S; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 22 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 23 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 24 EXPRESSION_SYSTEM_PLASMID: PKKT7 KEYWDS SINGLE STRAND DNA BINDING PROTEIN, PROTEIN DNA INTERACTIONS, SEQUENCE KEYWDS 2 SPECIFICITY, NONCOGNATE, OLIGONUCLEOTIDE AND OLIGOSACCHARIDE BINDING KEYWDS 3 FOLD, OB FOLD, TELOMERES, PROTEIN/DNA, DNA BINDING PROTEIN-DNA KEYWDS 4 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.L.THEOBALD,S.C.SCHULTZ REVDAT 4 16-NOV-11 1PH7 1 VERSN HETATM REVDAT 3 24-FEB-09 1PH7 1 VERSN REVDAT 2 25-NOV-03 1PH7 1 JRNL REVDAT 1 17-JUN-03 1PH7 0 JRNL AUTH D.L.THEOBALD,S.C.SCHULTZ JRNL TITL NUCLEOTIDE SHUFFLING AND SSDNA RECOGNITION IN OXYTRICHA NOVA JRNL TITL 2 TELOMERE END-BINDING PROTEIN COMPLEXES JRNL REF EMBO J. V. 22 4314 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 12912928 JRNL DOI 10.1093/EMBOJ/CDG415 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 136630.480 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 24336 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2426 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3477 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 408 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5439 REMARK 3 NUCLEIC ACID ATOMS : 736 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 502 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.15000 REMARK 3 B22 (A**2) : 4.15000 REMARK 3 B33 (A**2) : -8.29000 REMARK 3 B12 (A**2) : 8.89000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.36 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.80 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.320 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.140 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.710 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.520 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 21.54 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PH7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-03. REMARK 100 THE RCSB ID CODE IS RCSB019324. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 83 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24336 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 39.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 140.52833 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 281.05667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 210.79250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 351.32083 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 70.26417 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 140.52833 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 281.05667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 351.32083 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 210.79250 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 70.26417 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, D, H, A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1260 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1258 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 DT G 13 REMARK 465 DT H 13 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 ND2 ASN B 130 ND2 ASN B 130 12555 1.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 49 18.52 56.37 REMARK 500 ASP A 60 149.96 -171.46 REMARK 500 ALA A 61 142.46 -171.41 REMARK 500 ASN A 68 -160.12 -161.77 REMARK 500 GLU A 70 -3.80 -173.81 REMARK 500 LEU A 83 93.92 -168.00 REMARK 500 TYR A 84 -16.13 -160.33 REMARK 500 GLN A 87 89.21 -45.92 REMARK 500 LYS A 89 -54.39 -156.99 REMARK 500 ARG A 124 64.82 65.52 REMARK 500 PHE A 141 20.10 -75.41 REMARK 500 TYR A 142 -83.74 -140.91 REMARK 500 SER A 173 139.55 -173.92 REMARK 500 SER A 176 178.28 65.44 REMARK 500 ILE A 186 -33.00 -38.16 REMARK 500 VAL A 205 -47.83 71.19 REMARK 500 ASP A 247 -166.78 -104.29 REMARK 500 SER A 275 96.40 71.90 REMARK 500 ASP A 315 155.09 -49.57 REMARK 500 ALA A 344 58.18 -100.78 REMARK 500 ARG A 392 -4.79 -51.68 REMARK 500 LYS A 393 -80.14 -90.49 REMARK 500 THR A 394 -2.14 -59.36 REMARK 500 ALA A 403 174.01 70.89 REMARK 500 LYS A 406 -21.30 -38.40 REMARK 500 ASN A 426 33.54 -89.71 REMARK 500 ASN A 450 96.25 -61.77 REMARK 500 ASN B 24 48.71 -109.51 REMARK 500 GLU B 25 42.23 38.29 REMARK 500 SER B 46 -10.24 -144.18 REMARK 500 TYR B 47 140.36 -171.06 REMARK 500 TYR B 56 -53.41 -133.18 REMARK 500 ASP B 85 -15.48 75.57 REMARK 500 THR B 107 43.90 -101.74 REMARK 500 GLN B 126 -9.40 55.02 REMARK 500 ASP B 167 47.67 36.09 REMARK 500 ASN B 168 74.75 -68.26 REMARK 500 ASP B 177 71.70 48.71 REMARK 500 ASP B 186 8.75 -69.63 REMARK 500 SER B 195 140.85 -34.17 REMARK 500 LYS B 196 -81.69 -57.73 REMARK 500 SER B 201 23.88 -141.58 REMARK 500 GLU B 207 109.09 -54.92 REMARK 500 GLN B 221 5.88 -67.70 REMARK 500 GLU B 222 -16.54 -142.23 REMARK 500 LYS B 223 65.68 -166.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H1002 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG H 2 O6 REMARK 620 2 DG H 1 O6 90.9 REMARK 620 3 DG H 11 O6 140.7 128.1 REMARK 620 4 DG G 3 O6 92.8 101.0 85.1 REMARK 620 5 DG G 10 O6 92.3 115.5 68.4 143.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H1003 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG G 11 O6 REMARK 620 2 DG H 10 O6 108.9 REMARK 620 3 DG G 2 O6 147.5 85.2 REMARK 620 4 DG G 11 N1 49.5 61.5 143.6 REMARK 620 5 DG H 3 O6 93.0 145.2 63.2 141.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H1004 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG H 9 O6 REMARK 620 2 DG H 4 O6 115.4 REMARK 620 3 DG G 12 O6 76.1 73.8 REMARK 620 4 DT H 7 O2 93.1 119.6 165.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1005 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OTC RELATED DB: PDB REMARK 900 SAME PROTEIN (ALPHA AND BETA SUBUNITS) COMPLEXED WITH REMARK 900 COGNATE SSDNA GGGGTTTTGGGG REMARK 900 RELATED ID: 1JB7 RELATED DB: PDB REMARK 900 SAME PROTEIN (ALPHA AND BETA SUBUNITS) COMPLEXED WITH REMARK 900 COGNATE SSDNA GGGGTTTTGGGG REMARK 900 RELATED ID: 1KIX RELATED DB: PDB REMARK 900 DIMER OF ALPHA SUBUNIT ALONE COMPLEXED WITH TTTTGGGG REMARK 900 RELATED ID: 1K8G RELATED DB: PDB REMARK 900 35 KDA N-TERMINAL FRAGMENT OF ALPHA SUBUNIT ALONE COMPLEXED REMARK 900 WITH TTGGGG REMARK 900 RELATED ID: 1PA6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGAGG REMARK 900 RELATED ID: 1PH1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA REMARK 900 GGGGTTTTGGGGT REMARK 900 RELATED ID: 1PH2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTG REMARK 900 RELATED ID: 1PH3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGTG REMARK 900 RELATED ID: 1PH4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGCG REMARK 900 RELATED ID: 1PH5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA REMARK 900 GGGGTTTTG(3DR)GG REMARK 900 RELATED ID: 1PH6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGTGG REMARK 900 RELATED ID: 1PH8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGCGG REMARK 900 RELATED ID: 1PH9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGAGG REMARK 900 RELATED ID: 1PHJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GG(3DR) REMARK 900 GTTTTGGGG DBREF 1PH7 A 36 495 UNP P29549 TEBA_OXYNO 36 495 DBREF 1PH7 B 9 224 UNP P16458 TEBB_OXYNO 9 224 DBREF 1PH7 G 1 13 PDB 1PH7 1PH7 1 13 DBREF 1PH7 D 2 12 PDB 1PH7 1PH7 2 12 DBREF 1PH7 H 1 13 PDB 1PH7 1PH7 1 13 SEQRES 1 G 13 DG DG DG DG DT DT DT DT DG DG DG DG DT SEQRES 1 D 11 DG DG DG DT DT DT DT DG DI DG DG SEQRES 1 H 13 DG DG DG DG DT DT DT DT DG DG DG DG DT SEQRES 1 A 460 TYR GLU TYR VAL GLU LEU ALA LYS ALA SER LEU THR SER SEQRES 2 A 460 ALA GLN PRO GLN HIS PHE TYR ALA VAL VAL ILE ASP ALA SEQRES 3 A 460 THR PHE PRO TYR LYS THR ASN GLN GLU ARG TYR ILE CYS SEQRES 4 A 460 SER LEU LYS ILE VAL ASP PRO THR LEU TYR LEU LYS GLN SEQRES 5 A 460 GLN LYS GLY ALA GLY ASP ALA SER ASP TYR ALA THR LEU SEQRES 6 A 460 VAL LEU TYR ALA LYS ARG PHE GLU ASP LEU PRO ILE ILE SEQRES 7 A 460 HIS ARG ALA GLY ASP ILE ILE ARG VAL HIS ARG ALA THR SEQRES 8 A 460 LEU ARG LEU TYR ASN GLY GLN ARG GLN PHE ASN ALA ASN SEQRES 9 A 460 VAL PHE TYR SER SER SER TRP ALA LEU PHE SER THR ASP SEQRES 10 A 460 LYS ARG SER VAL THR GLN GLU ILE ASN ASN GLN ASP ALA SEQRES 11 A 460 VAL SER ASP THR THR PRO PHE SER PHE SER SER LYS HIS SEQRES 12 A 460 ALA THR ILE GLU LYS ASN GLU ILE SER ILE LEU GLN ASN SEQRES 13 A 460 LEU ARG LYS TRP ALA ASN GLN TYR PHE SER SER TYR SER SEQRES 14 A 460 VAL ILE SER SER ASP MET TYR THR ALA LEU ASN LYS ALA SEQRES 15 A 460 GLN ALA GLN LYS GLY ASP PHE ASP VAL VAL ALA LYS ILE SEQRES 16 A 460 LEU GLN VAL HIS GLU LEU ASP GLU TYR THR ASN GLU LEU SEQRES 17 A 460 LYS LEU LYS ASP ALA SER GLY GLN VAL PHE TYR THR LEU SEQRES 18 A 460 SER LEU LYS LEU LYS PHE PRO HIS VAL ARG THR GLY GLU SEQRES 19 A 460 VAL VAL ARG ILE ARG SER ALA THR TYR ASP GLU THR SER SEQRES 20 A 460 THR GLN LYS LYS VAL LEU ILE LEU SER HIS TYR SER ASN SEQRES 21 A 460 ILE ILE THR PHE ILE GLN SER SER LYS LEU ALA LYS GLU SEQRES 22 A 460 LEU ARG ALA LYS ILE GLN ASP ASP HIS SER VAL GLU VAL SEQRES 23 A 460 ALA SER LEU LYS LYS ASN VAL SER LEU ASN ALA VAL VAL SEQRES 24 A 460 LEU THR GLU VAL ASP LYS LYS HIS ALA ALA LEU PRO SER SEQRES 25 A 460 THR SER LEU GLN ASP LEU PHE HIS HIS ALA ASP SER ASP SEQRES 26 A 460 LYS GLU LEU GLN ALA GLN ASP THR PHE ARG THR GLN PHE SEQRES 27 A 460 TYR VAL THR LYS ILE GLU PRO SER ASP VAL LYS GLU TRP SEQRES 28 A 460 VAL LYS GLY TYR ASP ARG LYS THR LYS LYS SER SER SER SEQRES 29 A 460 LEU LYS GLY ALA SER GLY LYS GLY ASP ASN ILE PHE GLN SEQRES 30 A 460 VAL GLN PHE LEU VAL LYS ASP ALA SER THR GLN LEU ASN SEQRES 31 A 460 ASN ASN THR TYR ARG VAL LEU LEU TYR THR GLN ASP GLY SEQRES 32 A 460 LEU GLY ALA ASN PHE PHE ASN VAL LYS ALA ASP ASN LEU SEQRES 33 A 460 HIS LYS ASN ALA ASP ALA ARG LYS LYS LEU GLU ASP SER SEQRES 34 A 460 ALA GLU LEU LEU THR LYS PHE ASN SER TYR VAL ASP ALA SEQRES 35 A 460 VAL VAL GLU ARG ARG ASN GLY PHE TYR LEU ILE LYS ASP SEQRES 36 A 460 THR LYS LEU ILE TYR SEQRES 1 B 216 GLN GLN GLN SER ALA PHE LYS GLN LEU TYR THR GLU LEU SEQRES 2 B 216 PHE ASN ASN GLU GLY ASP PHE SER LYS VAL SER SER ASN SEQRES 3 B 216 LEU LYS LYS PRO LEU LYS CYS TYR VAL LYS GLU SER TYR SEQRES 4 B 216 PRO HIS PHE LEU VAL THR ASP GLY TYR PHE PHE VAL ALA SEQRES 5 B 216 PRO TYR PHE THR LYS GLU ALA VAL ASN GLU PHE HIS ALA SEQRES 6 B 216 LYS PHE PRO ASN VAL ASN ILE VAL ASP LEU THR ASP LYS SEQRES 7 B 216 VAL ILE VAL ILE ASN ASN TRP SER LEU GLU LEU ARG ARG SEQRES 8 B 216 VAL ASN SER ALA GLU VAL PHE THR SER TYR ALA ASN LEU SEQRES 9 B 216 GLU ALA ARG LEU ILE VAL HIS SER PHE LYS PRO ASN LEU SEQRES 10 B 216 GLN GLU ARG LEU ASN PRO THR ARG TYR PRO VAL ASN LEU SEQRES 11 B 216 PHE ARG ASP ASP GLU PHE LYS THR THR ILE GLN HIS PHE SEQRES 12 B 216 ARG HIS THR ALA LEU GLN ALA ALA ILE ASN LYS THR VAL SEQRES 13 B 216 LYS GLY ASP ASN LEU VAL ASP ILE SER LYS VAL ALA ASP SEQRES 14 B 216 ALA ALA GLY LYS LYS GLY LYS VAL ASP ALA GLY ILE VAL SEQRES 15 B 216 LYS ALA SER ALA SER LYS GLY ASP GLU PHE SER ASP PHE SEQRES 16 B 216 SER PHE LYS GLU GLY ASN THR ALA THR LEU LYS ILE ALA SEQRES 17 B 216 ASP ILE PHE VAL GLN GLU LYS GLY HET NA H1002 1 HET NA H1003 1 HET NA H1004 1 HET CL A1005 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 6 NA 3(NA 1+) FORMUL 9 CL CL 1- FORMUL 10 HOH *502(H2 O) HELIX 1 1 ARG A 106 LEU A 110 5 5 HELIX 2 2 SER A 155 ASN A 162 1 8 HELIX 3 3 GLU A 185 TYR A 203 1 19 HELIX 4 4 SER A 207 TYR A 211 5 5 HELIX 5 5 LYS A 216 GLN A 220 5 5 HELIX 6 6 SER A 303 ILE A 313 1 11 HELIX 7 7 HIS A 317 LEU A 324 1 8 HELIX 8 8 LYS A 340 ALA A 343 5 4 HELIX 9 9 SER A 349 HIS A 356 1 8 HELIX 10 10 ASP A 382 GLU A 385 5 4 HELIX 11 11 ASP A 419 GLN A 423 5 5 HELIX 12 12 ASN A 454 LYS A 470 1 17 HELIX 13 13 SER B 12 ASN B 24 1 13 HELIX 14 14 SER B 32 LYS B 36 5 5 HELIX 15 15 THR B 64 PHE B 75 1 12 HELIX 16 16 ASN B 79 LEU B 83 5 5 HELIX 17 17 ASP B 141 VAL B 164 1 24 HELIX 18 18 ASP B 171 VAL B 175 5 5 HELIX 19 19 LYS B 184 ALA B 187 5 4 HELIX 20 20 ALA B 216 GLY B 224 1 9 SHEET 1 A 6 TYR A 65 LYS A 66 0 SHEET 2 A 6 TYR A 72 VAL A 79 -1 O ILE A 73 N TYR A 65 SHEET 3 A 6 GLN A 52 ALA A 61 -1 N ASP A 60 O LYS A 77 SHEET 4 A 6 ILE A 119 TYR A 130 -1 O ALA A 125 N GLN A 52 SHEET 5 A 6 SER A 145 PHE A 149 -1 O PHE A 149 N ILE A 119 SHEET 6 A 6 SER A 173 PHE A 174 -1 O SER A 173 N LEU A 148 SHEET 1 B 7 TYR A 65 LYS A 66 0 SHEET 2 B 7 TYR A 72 VAL A 79 -1 O ILE A 73 N TYR A 65 SHEET 3 B 7 ALA A 98 ALA A 104 -1 O LEU A 100 N LEU A 76 SHEET 4 B 7 GLN A 133 ASN A 139 1 O ALA A 138 N TYR A 103 SHEET 5 B 7 ILE A 119 TYR A 130 -1 N THR A 126 O ASN A 137 SHEET 6 B 7 SER A 145 PHE A 149 -1 O PHE A 149 N ILE A 119 SHEET 7 B 7 SER A 173 PHE A 174 -1 O SER A 173 N LEU A 148 SHEET 1 C 6 ARG A 115 ALA A 116 0 SHEET 2 C 6 LEU A 288 PHE A 299 1 O THR A 298 N ALA A 116 SHEET 3 C 6 VAL A 270 TYR A 278 -1 N THR A 277 O ILE A 289 SHEET 4 C 6 PHE A 224 ASP A 237 -1 N VAL A 226 O ILE A 273 SHEET 5 C 6 THR A 240 LYS A 246 -1 O LYS A 246 N LYS A 229 SHEET 6 C 6 VAL A 252 LEU A 258 -1 O SER A 257 N ASN A 241 SHEET 1 D 6 SER A 397 SER A 398 0 SHEET 2 D 6 VAL A 387 TYR A 390 -1 N GLY A 389 O SER A 398 SHEET 3 D 6 ASP A 408 LYS A 418 -1 O ASP A 408 N TYR A 390 SHEET 4 D 6 THR A 368 GLU A 379 -1 N GLU A 379 O GLN A 414 SHEET 5 D 6 SER A 473 ARG A 482 -1 O VAL A 479 N PHE A 369 SHEET 6 D 6 VAL A 333 VAL A 334 1 N VAL A 333 O TYR A 474 SHEET 1 E 5 SER A 397 SER A 398 0 SHEET 2 E 5 VAL A 387 TYR A 390 -1 N GLY A 389 O SER A 398 SHEET 3 E 5 ASP A 408 LYS A 418 -1 O ASP A 408 N TYR A 390 SHEET 4 E 5 ASN A 427 TYR A 434 -1 O TYR A 429 N VAL A 417 SHEET 5 E 5 ILE B 189 LYS B 191 -1 O VAL B 190 N THR A 428 SHEET 1 F 5 ILE B 189 LYS B 191 0 SHEET 2 F 5 ASN A 427 TYR A 434 -1 N THR A 428 O VAL B 190 SHEET 3 F 5 PHE A 485 LYS A 489 1 O ILE A 488 N LEU A 432 SHEET 4 F 5 SER A 473 ARG A 482 -1 N ARG A 482 O PHE A 485 SHEET 5 F 5 VAL A 333 VAL A 334 1 N VAL A 333 O TYR A 474 SHEET 1 G 2 THR A 336 VAL A 338 0 SHEET 2 G 2 THR A 491 LEU A 493 -1 O LYS A 492 N GLU A 337 SHEET 1 H 7 PRO B 61 PHE B 63 0 SHEET 2 H 7 LEU B 112 ASN B 124 1 O LEU B 116 N TYR B 62 SHEET 3 H 7 VAL B 87 ARG B 99 -1 N ASN B 92 O HIS B 119 SHEET 4 H 7 LEU B 39 SER B 46 -1 N LEU B 39 O ILE B 90 SHEET 5 H 7 PHE B 50 THR B 53 -1 O THR B 53 N TYR B 42 SHEET 6 H 7 PHE B 57 VAL B 59 -1 O VAL B 59 N VAL B 52 SHEET 7 H 7 VAL B 136 ASN B 137 1 O VAL B 136 N PHE B 58 LINK NA NA H1002 O6 DG H 2 1555 1555 2.17 LINK NA NA H1002 O6 DG H 1 1555 1555 2.49 LINK NA NA H1002 O6 DG H 11 1555 1555 2.53 LINK NA NA H1003 O6 DG G 11 1555 1555 2.23 LINK NA NA H1003 O6 DG H 10 1555 1555 2.26 LINK NA NA H1004 O6 DG H 9 1555 1555 2.25 LINK NA NA H1004 O6 DG H 4 1555 1555 2.47 LINK NA NA H1004 O6 DG G 12 1555 1555 2.26 LINK O6 DG G 2 NA NA H1003 1555 1555 2.91 LINK O6 DG G 3 NA NA H1002 1555 1555 2.63 LINK O6 DG G 10 NA NA H1002 1555 1555 2.69 LINK N1 DG G 11 NA NA H1003 1555 1555 2.99 LINK O6 DG H 3 NA NA H1003 1555 1555 2.68 LINK O2 DT H 7 NA NA H1004 1555 1555 2.89 CISPEP 1 GLU A 379 PRO A 380 0 1.66 CISPEP 2 TYR B 47 PRO B 48 0 0.26 SITE 1 AC1 7 DG G 3 DG G 4 DG G 9 DG G 10 SITE 2 AC1 7 DG H 1 DG H 2 DG H 11 SITE 1 AC2 9 DG G 1 DG G 2 DG G 11 DG G 12 SITE 2 AC2 9 DG H 2 DG H 3 DG H 4 DG H 9 SITE 3 AC2 9 DG H 10 SITE 1 AC3 6 DG G 1 DG G 12 DG H 4 DT H 7 SITE 2 AC3 6 DG H 9 HOH H 501 SITE 1 AC4 4 ARG A 481 ASN A 483 GLY A 484 GLY B 183 CRYST1 93.194 93.194 421.585 90.00 90.00 120.00 P 61 2 2 24 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010730 0.006195 0.000000 0.00000 SCALE2 0.000000 0.012390 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002372 0.00000