PDB Short entry for 4F5Q HEADER TRANSFERASE, LYASE/DNA 13-MAY-12 4F5Q TITLE CLOSED TERNARY COMPLEX OF R283K DNA POLYMERASE BETA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7, 4.2.99.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*G)-3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'); COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 17 3'); COMPND 18 CHAIN: T; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TAP56; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PWL11; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: POLYDEOXYRIBONUCLEOTIDE FROM IDT; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630; SOURCE 20 OTHER_DETAILS: POLYDEOXYRIBONUCLEOTIDE FROM IDT; SOURCE 21 MOL_ID: 4; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 24 ORGANISM_TAXID: 32630; SOURCE 25 OTHER_DETAILS: POLYDEOXYRIBONUCLEOTIDE FROM IDT KEYWDS TRANSFERASE, LYASE/DNA, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,W.A.BEARD,S.H.WILSON REVDAT 3 13-SEP-23 4F5Q 1 REMARK SEQADV LINK REVDAT 2 17-JUL-19 4F5Q 1 REMARK REVDAT 1 12-DEC-12 4F5Q 0 JRNL AUTH B.D.FREUDENTHAL,W.A.BEARD,S.H.WILSON JRNL TITL STRUCTURES OF DNTP INTERMEDIATE STATES DURING DNA POLYMERASE JRNL TITL 2 ACTIVE SITE ASSEMBLY. JRNL REF STRUCTURE V. 20 1829 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 22959623 JRNL DOI 10.1016/J.STR.2012.08.008 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.9 REMARK 3 NUMBER OF REFLECTIONS : 17616 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1719 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 21.1055 - 5.1185 1.00 1558 172 0.2230 0.2689 REMARK 3 2 5.1185 - 4.0723 0.89 1373 145 0.1558 0.1908 REMARK 3 3 4.0723 - 3.5603 0.90 1390 133 0.1645 0.2570 REMARK 3 4 3.5603 - 3.2360 0.97 1474 158 0.2064 0.2566 REMARK 3 5 3.2360 - 3.0048 0.94 1448 155 0.2162 0.2923 REMARK 3 6 3.0048 - 2.8281 0.90 1362 156 0.2318 0.3222 REMARK 3 7 2.8281 - 2.6867 0.85 1284 142 0.2508 0.3343 REMARK 3 8 2.6867 - 2.5700 0.85 1272 136 0.2434 0.3189 REMARK 3 9 2.5700 - 2.4712 0.82 1274 149 0.2936 0.3798 REMARK 3 10 2.4712 - 2.3861 0.82 1226 116 0.2990 0.4426 REMARK 3 11 2.3861 - 2.3115 0.84 1267 140 0.2962 0.3954 REMARK 3 12 2.3115 - 2.2456 0.64 969 117 0.3698 0.4379 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 46.57 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3385 REMARK 3 ANGLE : 0.981 4704 REMARK 3 CHIRALITY : 0.055 513 REMARK 3 PLANARITY : 0.003 491 REMARK 3 DIHEDRAL : 19.863 1319 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 10:117) REMARK 3 ORIGIN FOR THE GROUP (A): 25.5232 -0.5780 10.1571 REMARK 3 T TENSOR REMARK 3 T11: 0.0361 T22: 0.0583 REMARK 3 T33: 0.0725 T12: 0.0062 REMARK 3 T13: 0.0493 T23: -0.0200 REMARK 3 L TENSOR REMARK 3 L11: 0.1878 L22: 0.0735 REMARK 3 L33: 0.2247 L12: 0.0570 REMARK 3 L13: 0.0546 L23: -0.0913 REMARK 3 S TENSOR REMARK 3 S11: -0.0377 S12: -0.0127 S13: -0.1117 REMARK 3 S21: 0.0137 S22: 0.0235 S23: -0.0161 REMARK 3 S31: 0.0070 S32: 0.0113 S33: 0.0165 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 118:275) REMARK 3 ORIGIN FOR THE GROUP (A): -1.2957 9.6669 15.0499 REMARK 3 T TENSOR REMARK 3 T11: 0.0024 T22: 0.0797 REMARK 3 T33: 0.0736 T12: -0.0200 REMARK 3 T13: 0.0234 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 0.0224 L22: 0.2272 REMARK 3 L33: 0.1881 L12: -0.0311 REMARK 3 L13: -0.0474 L23: -0.0563 REMARK 3 S TENSOR REMARK 3 S11: 0.0309 S12: 0.0135 S13: -0.0188 REMARK 3 S21: 0.0187 S22: 0.0068 S23: 0.1301 REMARK 3 S31: -0.0023 S32: -0.0972 S33: -0.0348 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 276:335) REMARK 3 ORIGIN FOR THE GROUP (A): 6.4842 8.9303 -9.2876 REMARK 3 T TENSOR REMARK 3 T11: 0.2868 T22: 0.5285 REMARK 3 T33: 0.2978 T12: -0.0073 REMARK 3 T13: -0.0000 T23: -0.0242 REMARK 3 L TENSOR REMARK 3 L11: 0.5073 L22: 0.1306 REMARK 3 L33: 0.1212 L12: 0.1978 REMARK 3 L13: -0.1268 L23: -0.0313 REMARK 3 S TENSOR REMARK 3 S11: -0.0681 S12: 0.3978 S13: -0.0182 REMARK 3 S21: -0.0834 S22: 0.1142 S23: -0.0139 REMARK 3 S31: 0.0125 S32: -0.0215 S33: -0.0447 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4F5Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072488. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : MIRRORS VARIMAXHF REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 112322 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 28.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.09800 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) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.59900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.380 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: 2FMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM IMIDAZOLE, 350MM SODIUM ACETATE, REMARK 280 18% PEG3350, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 38.81450 REMARK 290 SMTRY3 2 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 BIOLOGICAL ASSEMBLY IS A MONOMER IN EACH ASYMETRIC 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, P, T 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 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 REMARK 465 THR A 205 REMARK 465 LYS A 206 REMARK 465 GLN A 207 REMARK 465 PRO A 208 REMARK 465 ASN A 245 REMARK 465 ASP A 246 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 LYS A 244 CG CD CE NZ REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 VAL A 303 CG1 CG2 REMARK 470 VAL A 306 CG1 CG2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 40 N CA C O CB CG CD REMARK 480 ARG A 40 NE CZ NH1 NH2 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 -0.124 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 DT D 2 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DG D 4 O4' - C1' - N9 ANGL. DEV. = -5.0 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 LEU A 11 -71.04 -89.45 REMARK 500 CYS A 178 -154.56 -118.06 REMARK 500 GLU A 295 1.44 -62.54 REMARK 500 GLN A 324 47.45 77.21 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 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 98.9 REMARK 620 3 VAL A 65 O 96.1 95.0 REMARK 620 4 HOH A 573 O 84.3 160.6 103.7 REMARK 620 5 DC D 3 OP1 164.5 86.9 97.8 85.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 96.0 REMARK 620 3 ILE A 106 O 88.7 84.3 REMARK 620 4 HOH A 536 O 90.4 96.2 179.0 REMARK 620 5 DG P 9 OP1 163.8 99.6 97.1 83.6 REMARK 620 6 HOH P 106 O 78.5 164.4 81.0 98.4 87.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 90.7 REMARK 620 3 6CF A 403 O3G 86.4 175.1 REMARK 620 4 6CF A 403 O2B 169.1 91.6 90.5 REMARK 620 5 6CF A 403 O1A 106.8 85.0 99.6 84.1 REMARK 620 6 HOH A 505 O 78.0 80.7 94.8 91.8 165.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD2 REMARK 620 2 ASP A 192 OD1 102.5 REMARK 620 3 ASP A 256 OD2 92.4 91.1 REMARK 620 4 6CF A 403 O1A 93.1 92.6 172.5 REMARK 620 5 HOH A 572 O 74.5 176.3 91.2 85.5 REMARK 620 6 DC P 10 O3' 152.2 105.2 84.6 88.2 78.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 6CF A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F5R RELATED DB: PDB REMARK 900 RELATED ID: 4F5P RELATED DB: PDB REMARK 900 RELATED ID: 4F5O RELATED DB: PDB REMARK 900 RELATED ID: 4F5N RELATED DB: PDB DBREF 4F5Q A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 4F5Q T 1 16 PDB 4F5Q 4F5Q 1 16 DBREF 4F5Q P 1 10 PDB 4F5Q 4F5Q 1 10 DBREF 4F5Q D 1 5 PDB 4F5Q 4F5Q 1 5 SEQADV 4F5Q LYS A 283 UNP P06746 ARG 283 ENGINEERED MUTATION SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET LYS ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU SEQRES 1 D 5 DG DT DC DG DG SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DC SEQRES 1 T 16 DC DC DG DA DC DG DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC HET MN A 401 1 HET MN A 402 1 HET 6CF A 403 30 HET NA A 404 1 HET NA A 405 1 HETNAM MN MANGANESE (II) ION HETNAM 6CF 2'-DEOXY-5'-O-[(S)-{DIFLUORO[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 6CF PHOSPHORYL]METHYL}(HYDROXY)PHOSPHORYL]CYTIDINE HETNAM NA SODIUM ION FORMUL 5 MN 2(MN 2+) FORMUL 7 6CF C10 H16 F2 N3 O12 P3 FORMUL 8 NA 2(NA 1+) FORMUL 10 HOH *107(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 LYS A 48 1 17 HELIX 3 3 SER A 55 LYS A 61 1 7 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 ASP A 91 1 10 HELIX 6 6 ASP A 91 THR A 101 1 11 HELIX 7 7 GLY A 107 GLU A 117 1 11 HELIX 8 8 THR A 121 ASN A 128 1 8 HELIX 9 9 GLU A 129 LEU A 132 5 4 HELIX 10 10 ASN A 133 TYR A 142 1 10 HELIX 11 11 TYR A 142 LYS A 148 1 7 HELIX 12 12 ARG A 152 LYS A 168 1 17 HELIX 13 13 GLY A 179 ARG A 182 5 4 HELIX 14 14 LEU A 210 VAL A 221 1 12 HELIX 15 15 PRO A 261 ASP A 263 5 3 HELIX 16 16 GLN A 264 GLY A 274 1 11 HELIX 17 17 SER A 275 GLU A 288 1 14 HELIX 18 18 SER A 315 GLN A 324 1 10 HELIX 19 19 GLU A 329 ARG A 333 5 5 SHEET 1 A 2 ILE A 150 PRO A 151 0 SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 B 5 ILE A 174 CYS A 178 0 SHEET 2 B 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 B 5 ARG A 253 LEU A 259 1 O ASP A 256 N VAL A 193 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N GLY A 237 O ILE A 255 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N LEU A 228 O MET A 236 SHEET 1 C 2 PHE A 291 ILE A 293 0 SHEET 2 C 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O LYS A 60 NA NA A 404 1555 1555 2.52 LINK O LEU A 62 NA NA A 404 1555 1555 2.45 LINK O VAL A 65 NA NA A 404 1555 1555 2.21 LINK O THR A 101 NA NA A 405 1555 1555 2.22 LINK O VAL A 103 NA NA A 405 1555 1555 2.34 LINK O ILE A 106 NA NA A 405 1555 1555 2.79 LINK OD1 ASP A 190 MN MN A 401 1555 1555 2.09 LINK OD2 ASP A 190 MN MN A 402 1555 1555 2.03 LINK OD2 ASP A 192 MN MN A 401 1555 1555 2.03 LINK OD1 ASP A 192 MN MN A 402 1555 1555 2.10 LINK OD2 ASP A 256 MN MN A 402 1555 1555 2.19 LINK MN MN A 401 O3G 6CF A 403 1555 1555 2.01 LINK MN MN A 401 O2B 6CF A 403 1555 1555 2.05 LINK MN MN A 401 O1A 6CF A 403 1555 1555 2.07 LINK MN MN A 401 O HOH A 505 1555 1555 2.26 LINK MN MN A 402 O1A 6CF A 403 1555 1555 2.20 LINK MN MN A 402 O HOH A 572 1555 1555 2.21 LINK MN MN A 402 O3' DC P 10 1555 1555 2.14 LINK NA NA A 404 O HOH A 573 1555 1555 2.38 LINK NA NA A 404 OP1 DC D 3 1555 1555 2.75 LINK NA NA A 405 O HOH A 536 1555 1555 2.12 LINK NA NA A 405 OP1 DG P 9 1555 1555 2.64 LINK NA NA A 405 O HOH P 106 1555 1555 2.93 CISPEP 1 GLY A 274 SER A 275 0 4.64 SITE 1 AC1 5 ASP A 190 ASP A 192 MN A 402 6CF A 403 SITE 2 AC1 5 HOH A 505 SITE 1 AC2 7 ASP A 190 ASP A 192 ASP A 256 MN A 401 SITE 2 AC2 7 6CF A 403 HOH A 572 DC P 10 SITE 1 AC3 19 GLY A 179 SER A 180 ARG A 183 SER A 188 SITE 2 AC3 19 GLY A 189 ASP A 190 ASP A 192 TYR A 271 SITE 3 AC3 19 PHE A 272 THR A 273 GLY A 274 ASP A 276 SITE 4 AC3 19 ASN A 279 MN A 401 MN A 402 HOH A 505 SITE 5 AC3 19 HOH A 572 DC P 10 DG T 6 SITE 1 AC4 5 LYS A 60 LEU A 62 VAL A 65 HOH A 573 SITE 2 AC4 5 DC D 3 SITE 1 AC5 6 THR A 101 VAL A 103 ILE A 106 HOH A 536 SITE 2 AC5 6 DG P 9 HOH P 106 CRYST1 55.139 77.629 54.953 90.00 114.20 90.00 P 1 21 1 2 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 0.018136 0.000000 0.008151 0.00000 SCALE2 0.000000 0.012882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019951 0.00000