PDB Short entry for 1XSP HEADER TRANSFERASE/DNA 19-OCT-04 1XSP TITLE CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE LAMBDA IN COMPLEX WITH TITLE 2 NICKED DNA AND PYROPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*GP*CP*CP*GP*TP*AP*CP*TP*G)-3'; COMPND 3 CHAIN: T; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*AP*GP*TP*AP*CP*G)-3'; COMPND 7 CHAIN: P; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(P*GP*CP*CP*G)-3'; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 15 CHAIN: A; COMPND 16 FRAGMENT: 39 KDA CATALYTIC C-TERMINAL DOMAIN; COMPND 17 SYNONYM: POL LAMBDA, DNA POLYMERASE BETA-2, POL BETA2; COMPND 18 EC: 2.7.7.7; COMPND 19 ENGINEERED: YES; COMPND 20 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: TEMPLATE DNA; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: PRIMER DNA; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: DOWNSTREAM PRIMER DNA; SOURCE 10 MOL_ID: 4; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: POLL; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PET22-B KEYWDS DNA POLYMERASE LAMBDA, PROTEIN-DNA COMPLEX, HELIX-HAIRPIN-HELIX, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.GARCIA-DIAZ,K.BEBENEK,J.M.KRAHN,T.A.KUNKEL,L.C.PEDERSEN REVDAT 5 14-FEB-24 1XSP 1 REMARK REVDAT 4 20-OCT-21 1XSP 1 REMARK SEQADV LINK REVDAT 3 24-JAN-18 1XSP 1 JRNL REVDAT 2 24-FEB-09 1XSP 1 VERSN REVDAT 1 18-JAN-05 1XSP 0 JRNL AUTH M.GARCIA-DIAZ,K.BEBENEK,J.M.KRAHN,T.A.KUNKEL,L.C.PEDERSEN JRNL TITL A CLOSED CONFORMATION FOR THE POL LAMBDA CATALYTIC CYCLE. JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 97 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 15608652 JRNL DOI 10.1038/NSMB876 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.GARCIA-DIAZ,K.BEBENEK,J.M.KRAHN,L.BLANCO,T.A.KUNKEL, REMARK 1 AUTH 2 L.C.PEDERSEN REMARK 1 TITL A STRUCTURAL SOLUTION FOR THE DNA POLYMERASE-LAMBDA REMARK 1 TITL 2 DEPENDENT REPAIR OF DNA GAPS WITH MINIMAL HOMOLOGY REMARK 1 REF MOL.CELL V. 13 561 2004 REMARK 1 REFN ISSN 1097-2765 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.GARCIA-DIAZ,K.BEBENEK,R.SABARIEGOS,O.DOMINGUEZ, REMARK 1 AUTH 2 J.RODRIGUEZ,T.KIRCHHOFF,E.GARCIA-PALOMERO,A.J.PICHER, REMARK 1 AUTH 3 R.JUAREZ,J.F.RUIZ,T.A.KUNKEL,L.BLANCO REMARK 1 TITL DNA POLYMERASE LAMBDA, A NOVEL DNA REPAIR ENZYME IN HUMAN REMARK 1 TITL 2 CELLS REMARK 1 REF J.BIOL.CHEM. V. 277 13184 2002 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 3 REMARK 1 AUTH K.BEBENEK,K.GARCIA-DIAZ,L.BLANCO,T.A.KUNKEL REMARK 1 TITL THE FRAMESHIFT INFIDELITY OF HUMAN DNA POLYMERASE LAMBDA. REMARK 1 TITL 2 IMPLICATIONS FOR FUNCTION. REMARK 1 REF J.BIOL.CHEM. V. 278 34685 2003 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.GARCIA-DIAZ,K.BEBENEK,T.A.KUNKEL,L.BLANCO REMARK 1 TITL IDENTIFICATION OF AN INTRINSIC 5'-DEOXYRIBOSE-5-PHOSPHATE REMARK 1 TITL 2 LYASE ACTIVITY IN HUMAN DNA POLYMERASE LAMBDA: A POSSIBLE REMARK 1 TITL 3 ROLE IN BASE EXCISION REPAIR REMARK 1 REF J.BIOL.CHEM. V. 276 34659 2001 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.20 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 141990.860 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 24337 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) : 0.206 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1165 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3337 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 152 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2527 REMARK 3 NUCLEIC ACID ATOMS : 446 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 334 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.30000 REMARK 3 B22 (A**2) : 9.87000 REMARK 3 B33 (A**2) : -2.58000 REMARK 3 B12 (A**2) : 0.00000 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.28 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) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.290 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) : 1.270 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.120 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.630 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.750 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 43.71 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 : PPI.PARAM REMARK 3 PARAMETER FILE 5 : ION.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : PPI.TOP REMARK 3 TOPOLOGY FILE 5 : ION.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XSP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25700 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-PROPANOL, SODIUM CITRATE, SODIUM REMARK 280 CHLORIDE, CACODYLATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 27.92250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.36000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.37900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.36000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.92250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.37900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: THE PROTEIN IS A MONOMER THUS THE ASYMMETRIC UNIT REMARK 300 REPRESENTS THE BIOLOGICAL UNIT 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, D, A 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 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 MET A 241 REMARK 465 ALA A 242 REMARK 465 GLN A 243 REMARK 465 PRO A 244 REMARK 465 SER A 245 REMARK 465 SER A 246 REMARK 465 GLN A 247 REMARK 465 LYS A 248 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 THR A 250 OG1 CG2 REMARK 470 VAL A 293 CG1 CG2 REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 SER A 319 OG REMARK 470 HIS A 321 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 322 CG CD1 CD2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 545 CG1 CG2 REMARK 470 TRP A 575 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 575 CZ3 CH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DG D 1 P DG D 1 OP3 -0.081 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 449 O - C - N ANGL. DEV. = -13.3 DEGREES 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 ASN A 251 95.54 -67.99 REMARK 500 ASN A 253 30.51 -146.00 REMARK 500 ASN A 407 87.34 -175.53 REMARK 500 CYS A 415 -136.69 -110.31 REMARK 500 ARG A 438 -31.90 -146.45 REMARK 500 GLU A 454 10.31 -69.39 REMARK 500 SER A 463 91.01 -163.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 449 -23.43 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 A 578 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH T 21 O REMARK 620 2 HOH T 44 O 105.9 REMARK 620 3 SER A 463 O 97.4 94.8 REMARK 620 4 HOH A 613 O 91.8 161.5 77.3 REMARK 620 5 HOH A 691 O 83.9 106.7 157.3 80.0 REMARK 620 6 HOH A 738 O 173.9 79.9 83.7 82.6 92.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 577 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA P 5 OP1 REMARK 620 2 HOH P 40 O 91.3 REMARK 620 3 HOH P 172 O 93.7 98.8 REMARK 620 4 SER A 339 O 163.4 73.5 95.1 REMARK 620 5 ILE A 341 O 96.8 164.0 94.4 96.6 REMARK 620 6 ALA A 344 O 89.1 82.9 176.7 82.6 83.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 576 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 7 OP1 REMARK 620 2 ASP A 427 OD1 74.7 REMARK 620 3 ASP A 429 OD2 78.8 90.9 REMARK 620 4 PPV A 579 O12 120.1 164.8 95.1 REMARK 620 5 PPV A 579 O22 76.6 133.6 118.1 54.1 REMARK 620 6 HOH A 608 O 150.1 83.1 81.8 84.0 133.0 REMARK 620 7 HOH A 686 O 92.2 80.8 169.1 94.7 64.7 104.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 576 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 577 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 578 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA D 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PPV A 579 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XSL RELATED DB: PDB REMARK 900 RELATED ID: 1XSN RELATED DB: PDB DBREF 1XSP A 242 575 UNP Q9UGP5 DPOL_HUMAN 242 575 DBREF 1XSP T 1 11 PDB 1XSP 1XSP 1 11 DBREF 1XSP P 1 7 PDB 1XSP 1XSP 1 7 DBREF 1XSP D 1 4 PDB 1XSP 1XSP 1 4 SEQADV 1XSP MET A 241 UNP Q9UGP5 INITIATING METHIONINE SEQADV 1XSP ALA A 543 UNP Q9UGP5 CYS 543 ENGINEERED MUTATION SEQRES 1 T 11 DC DG DG DC DC DG DT DA DC DT DG SEQRES 1 P 7 DC DA DG DT DA DC DG SEQRES 1 D 4 DG DC DC DG SEQRES 1 A 335 MET ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN SEQRES 2 A 335 LEU HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA SEQRES 3 A 335 TYR SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR SEQRES 4 A 335 ALA LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO SEQRES 5 A 335 VAL THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE SEQRES 6 A 335 GLY LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SEQRES 7 A 335 SER GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER SEQRES 8 A 335 VAL PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA SEQRES 9 A 335 GLY THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE SEQRES 10 A 335 ARG SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR SEQRES 11 A 335 THR GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE SEQRES 12 A 335 LEU GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU SEQRES 13 A 335 GLN THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY SEQRES 14 A 335 LEU LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS SEQRES 15 A 335 ALA THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO SEQRES 16 A 335 ASP GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU SEQRES 17 A 335 ASP SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU SEQRES 18 A 335 VAL SER GLN GLU GLU ASN GLY GLN GLN GLN LYS TYR LEU SEQRES 19 A 335 GLY VAL CYS ARG LEU PRO GLY PRO GLY ARG ARG HIS ARG SEQRES 20 A 335 ARG LEU ASP ILE ILE VAL VAL PRO TYR SER GLU PHE ALA SEQRES 21 A 335 CYS ALA LEU LEU TYR PHE THR GLY SER ALA HIS PHE ASN SEQRES 22 A 335 ARG SER MET ARG ALA LEU ALA LYS THR LYS GLY MET SER SEQRES 23 A 335 LEU SER GLU HIS ALA LEU SER THR ALA VAL VAL ARG ASN SEQRES 24 A 335 THR HIS GLY ALA LYS VAL GLY PRO GLY ARG VAL LEU PRO SEQRES 25 A 335 THR PRO THR GLU LYS ASP VAL PHE ARG LEU LEU GLY LEU SEQRES 26 A 335 PRO TYR ARG GLU PRO ALA GLU ARG ASP TRP HET NA D 503 1 HET NA A 576 1 HET NA A 577 1 HET NA A 578 1 HET PPV A 579 9 HETNAM NA SODIUM ION HETNAM PPV PYROPHOSPHATE FORMUL 5 NA 4(NA 1+) FORMUL 9 PPV H4 O7 P2 FORMUL 10 HOH *334(H2 O) HELIX 1 1 ASN A 253 GLY A 271 1 19 HELIX 2 2 ASP A 272 PHE A 289 1 18 HELIX 3 3 SER A 295 SER A 301 1 7 HELIX 4 4 GLY A 306 SER A 319 1 14 HELIX 5 5 LEU A 322 ILE A 328 5 7 HELIX 6 6 SER A 331 ASN A 340 1 10 HELIX 7 7 GLY A 345 GLN A 355 1 11 HELIX 8 8 SER A 359 ALA A 367 1 9 HELIX 9 9 THR A 370 HIS A 379 1 10 HELIX 10 10 SER A 381 GLU A 385 5 5 HELIX 11 11 ARG A 389 ALA A 405 1 17 HELIX 12 12 CYS A 415 ARG A 420 1 6 HELIX 13 13 ILE A 443 GLU A 454 1 12 HELIX 14 14 PRO A 495 SER A 497 5 3 HELIX 15 15 GLU A 498 GLY A 508 1 11 HELIX 16 16 SER A 509 LYS A 523 1 15 HELIX 17 17 THR A 555 LEU A 563 1 9 HELIX 18 18 GLU A 569 ARG A 573 5 5 SHEET 1 A 2 MET A 387 PRO A 388 0 SHEET 2 A 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 B 5 LEU A 411 ALA A 414 0 SHEET 2 B 5 VAL A 428 THR A 433 -1 O LEU A 431 N VAL A 413 SHEET 3 B 5 ARG A 487 VAL A 493 1 O ASP A 490 N VAL A 430 SHEET 4 B 5 LYS A 472 CYS A 477 -1 N CYS A 477 O ARG A 487 SHEET 5 B 5 LEU A 457 VAL A 462 -1 N THR A 458 O VAL A 476 SHEET 1 C 3 SER A 526 LEU A 527 0 SHEET 2 C 3 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 SHEET 3 C 3 ARG A 549 VAL A 550 -1 O ARG A 549 N THR A 534 SHEET 1 D 2 VAL A 537 ARG A 538 0 SHEET 2 D 2 LYS A 544 GLY A 546 -1 O VAL A 545 N VAL A 537 LINK O HOH T 21 NA NA A 578 1555 1555 2.85 LINK O HOH T 44 NA NA A 578 1555 1555 2.40 LINK OP1 DA P 5 NA NA A 577 1555 1555 2.42 LINK OP1 DG P 7 NA NA A 576 1555 1555 2.76 LINK O HOH P 40 NA NA A 577 1555 1555 2.90 LINK O HOH P 172 NA NA A 577 1555 1555 2.68 LINK OP1 DG D 1 NA NA D 503 1555 1555 2.59 LINK O SER A 339 NA NA A 577 1555 1555 2.55 LINK O ILE A 341 NA NA A 577 1555 1555 2.64 LINK O ALA A 344 NA NA A 577 1555 1555 2.57 LINK OD1 ASP A 427 NA NA A 576 1555 1555 2.37 LINK OD2 ASP A 429 NA NA A 576 1555 1555 2.41 LINK O SER A 463 NA NA A 578 1555 1555 2.41 LINK NA NA A 576 O12 PPV A 579 1555 1555 2.33 LINK NA NA A 576 O22 PPV A 579 1555 1555 3.00 LINK NA NA A 576 O HOH A 608 1555 1555 2.62 LINK NA NA A 576 O HOH A 686 1555 1555 2.52 LINK NA NA A 578 O HOH A 613 1555 1555 2.51 LINK NA NA A 578 O HOH A 691 1555 1555 2.70 LINK NA NA A 578 O HOH A 738 1555 1555 2.48 CISPEP 1 GLY A 508 SER A 509 0 -0.01 SITE 1 AC1 6 ASP A 427 ASP A 429 PPV A 579 HOH A 608 SITE 2 AC1 6 HOH A 686 DG P 7 SITE 1 AC2 6 SER A 339 ILE A 341 ALA A 344 DA P 5 SITE 2 AC2 6 HOH P 40 HOH P 172 SITE 1 AC3 6 SER A 463 HOH A 613 HOH A 691 HOH A 738 SITE 2 AC3 6 HOH T 21 HOH T 44 SITE 1 AC4 2 LYS A 324 DG D 1 SITE 1 AC5 11 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 2 AC5 11 GLY A 426 ASP A 429 NA A 576 HOH A 584 SITE 3 AC5 11 HOH A 631 HOH A 686 DG P 7 CRYST1 55.845 62.758 140.720 90.00 90.00 90.00 P 21 21 21 4 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 0.017907 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015934 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007106 0.00000