HEADER TRANSFERASE/DNA 28-JUL-20 7JKP TITLE HUMAN PRIMPOL MISINSERTING DATP OPPOSITE THE 8-OXOGUANINE LESION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED PRIMASE/POLYMERASE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HPRIMPOL1,COILED-COIL DOMAIN-CONTAINING PROTEIN 111; COMPND 5 EC: 2.7.7.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*AP*(8OG) COMPND 9 P*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3'); COMPND 10 CHAIN: C, G; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*CP*G)-3'); COMPND 14 CHAIN: D, H; COMPND 15 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: PRIMPOL, CCDC111; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS TRANSLESION, DNA SYNTHESIS, DNA REPLICATION, DNA DAMAGE, TRANSFERASE, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR O.RECHKOBLIT,A.K.AGGARWAL REVDAT 3 18-OCT-23 7JKP 1 REMARK REVDAT 2 14-JUL-21 7JKP 1 JRNL REVDAT 1 30-JUN-21 7JKP 0 JRNL AUTH O.RECHKOBLIT,R.E.JOHNSON,Y.K.GUPTA,L.PRAKASH,S.PRAKASH, JRNL AUTH 2 A.K.AGGARWAL JRNL TITL STRUCTURAL BASIS OF DNA SYNTHESIS OPPOSITE 8-OXOGUANINE BY JRNL TITL 2 HUMAN PRIMPOL PRIMASE-POLYMERASE. JRNL REF NAT COMMUN V. 12 4020 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34188055 JRNL DOI 10.1038/S41467-021-24317-Z REMARK 2 REMARK 2 RESOLUTION. 2.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 26648 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.307 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1332 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 69.1700 - 5.5836 0.94 2560 124 0.2142 0.2693 REMARK 3 2 5.5836 - 4.4321 0.96 2602 117 0.2096 0.2489 REMARK 3 3 4.4321 - 3.8719 0.94 2544 149 0.2175 0.2915 REMARK 3 4 3.8719 - 3.5179 0.95 2599 124 0.2429 0.3317 REMARK 3 5 3.5179 - 3.2658 0.95 2565 139 0.2568 0.3009 REMARK 3 6 3.2658 - 3.0732 0.94 2551 134 0.3000 0.3413 REMARK 3 7 3.0732 - 2.9193 0.96 2579 158 0.3050 0.3587 REMARK 3 8 2.9193 - 2.7922 0.97 2651 148 0.3309 0.3765 REMARK 3 9 2.7922 - 2.6847 0.97 2617 123 0.3785 0.4280 REMARK 3 10 2.6847 - 2.5921 0.76 2048 116 0.4809 0.5021 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 96.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.011 5514 REMARK 3 ANGLE : 0.495 7705 REMARK 3 CHIRALITY : 0.038 859 REMARK 3 PLANARITY : 0.002 787 REMARK 3 DIHEDRAL : 17.587 2989 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7JKP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250993. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979200 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27189 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.580 REMARK 200 RESOLUTION RANGE LOW (A) : 69.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 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 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: PHASER REMARK 200 STARTING MODEL: 5L2X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 225- 250 MM CACL2 16 -19% PEG 3350, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, G, H 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 ARG A 15 REMARK 465 ALA A 16 REMARK 465 SER A 17 REMARK 465 HIS A 18 REMARK 465 TYR A 19 REMARK 465 GLU A 20 REMARK 465 ARG A 21 REMARK 465 LYS A 22 REMARK 465 PRO A 23 REMARK 465 LEU A 24 REMARK 465 SER A 25 REMARK 465 SER A 26 REMARK 465 VAL A 27 REMARK 465 TYR A 28 REMARK 465 ARG A 29 REMARK 465 PRO A 30 REMARK 465 ARG A 31 REMARK 465 LEU A 32 REMARK 465 SER A 33 REMARK 465 LYS A 34 REMARK 465 PRO A 35 REMARK 465 GLY A 201 REMARK 465 SER A 202 REMARK 465 GLU A 203 REMARK 465 ASP A 204 REMARK 465 ASP A 205 REMARK 465 ASP A 206 REMARK 465 SER A 207 REMARK 465 ALA A 208 REMARK 465 PRO A 209 REMARK 465 GLU A 210 REMARK 465 THR A 211 REMARK 465 THR A 212 REMARK 465 GLY A 213 REMARK 465 HIS A 214 REMARK 465 GLY A 215 REMARK 465 PHE A 216 REMARK 465 PRO A 217 REMARK 465 HIS A 218 REMARK 465 PHE A 219 REMARK 465 SER A 220 REMARK 465 GLU A 221 REMARK 465 ALA A 222 REMARK 465 PRO A 223 REMARK 465 ALA A 224 REMARK 465 ARG A 225 REMARK 465 GLN A 226 REMARK 465 GLY A 227 REMARK 465 PHE A 228 REMARK 465 SER A 229 REMARK 465 PHE A 230 REMARK 465 ASN A 231 REMARK 465 LYS A 232 REMARK 465 MET A 233 REMARK 465 PHE A 234 REMARK 465 THR A 235 REMARK 465 GLU A 236 REMARK 465 LYS A 237 REMARK 465 ALA A 238 REMARK 465 THR A 239 REMARK 465 GLU A 240 REMARK 465 GLU A 241 REMARK 465 SER A 242 REMARK 465 TRP A 243 REMARK 465 THR A 244 REMARK 465 SER A 245 REMARK 465 ASN A 246 REMARK 465 SER A 247 REMARK 465 LYS A 248 REMARK 465 LYS A 249 REMARK 465 LEU A 250 REMARK 465 GLU A 251 REMARK 465 ARG A 252 REMARK 465 LEU A 253 REMARK 465 GLY A 254 REMARK 465 SER A 255 REMARK 465 ALA A 256 REMARK 465 GLU A 257 REMARK 465 GLN A 258 REMARK 465 SER A 259 REMARK 465 SER A 260 REMARK 465 PRO A 261 REMARK 465 SER A 349 REMARK 465 GLN A 350 REMARK 465 ASN A 351 REMARK 465 LYS A 352 REMARK 465 GLN A 353 REMARK 465 LYS A 354 REMARK 465 DC C 1 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 ARG B 3 REMARK 465 LYS B 4 REMARK 465 TRP B 5 REMARK 465 GLU B 6 REMARK 465 ALA B 7 REMARK 465 LYS B 8 REMARK 465 LEU B 9 REMARK 465 LYS B 10 REMARK 465 GLN B 11 REMARK 465 ILE B 12 REMARK 465 GLU B 13 REMARK 465 GLU B 14 REMARK 465 ARG B 15 REMARK 465 ALA B 16 REMARK 465 SER B 17 REMARK 465 HIS B 18 REMARK 465 TYR B 19 REMARK 465 GLU B 20 REMARK 465 ARG B 21 REMARK 465 LYS B 22 REMARK 465 PRO B 23 REMARK 465 LEU B 24 REMARK 465 SER B 25 REMARK 465 SER B 26 REMARK 465 VAL B 27 REMARK 465 TYR B 28 REMARK 465 ARG B 29 REMARK 465 PRO B 30 REMARK 465 ARG B 31 REMARK 465 LEU B 32 REMARK 465 SER B 33 REMARK 465 LYS B 34 REMARK 465 PRO B 35 REMARK 465 GLU B 36 REMARK 465 GLY B 201 REMARK 465 SER B 202 REMARK 465 GLU B 203 REMARK 465 ASP B 204 REMARK 465 ASP B 205 REMARK 465 ASP B 206 REMARK 465 SER B 207 REMARK 465 ALA B 208 REMARK 465 PRO B 209 REMARK 465 GLU B 210 REMARK 465 THR B 211 REMARK 465 THR B 212 REMARK 465 GLY B 213 REMARK 465 HIS B 214 REMARK 465 GLY B 215 REMARK 465 PHE B 216 REMARK 465 PRO B 217 REMARK 465 HIS B 218 REMARK 465 PHE B 219 REMARK 465 SER B 220 REMARK 465 GLU B 221 REMARK 465 ALA B 222 REMARK 465 PRO B 223 REMARK 465 ALA B 224 REMARK 465 ARG B 225 REMARK 465 GLN B 226 REMARK 465 GLY B 227 REMARK 465 PHE B 228 REMARK 465 SER B 229 REMARK 465 PHE B 230 REMARK 465 ASN B 231 REMARK 465 LYS B 232 REMARK 465 MET B 233 REMARK 465 PHE B 234 REMARK 465 THR B 235 REMARK 465 GLU B 236 REMARK 465 LYS B 237 REMARK 465 ALA B 238 REMARK 465 THR B 239 REMARK 465 GLU B 240 REMARK 465 GLU B 241 REMARK 465 SER B 242 REMARK 465 TRP B 243 REMARK 465 THR B 244 REMARK 465 SER B 245 REMARK 465 ASN B 246 REMARK 465 SER B 247 REMARK 465 LYS B 248 REMARK 465 LYS B 249 REMARK 465 LEU B 250 REMARK 465 GLU B 251 REMARK 465 ARG B 252 REMARK 465 LEU B 253 REMARK 465 GLY B 254 REMARK 465 SER B 255 REMARK 465 ALA B 256 REMARK 465 GLU B 257 REMARK 465 GLN B 258 REMARK 465 SER B 259 REMARK 465 SER B 260 REMARK 465 PRO B 261 REMARK 465 SER B 349 REMARK 465 GLN B 350 REMARK 465 ASN B 351 REMARK 465 LYS B 352 REMARK 465 GLN B 353 REMARK 465 LYS B 354 REMARK 465 DC G 1 REMARK 465 DG H 2 REMARK 465 DG H 3 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 ASN A 2 CG OD1 ND2 REMARK 470 ARG A 3 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 4 CG CD CE NZ REMARK 470 TRP A 5 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 5 CZ3 CH2 REMARK 470 GLU A 6 CG CD OE1 OE2 REMARK 470 LYS A 8 CG CD CE NZ REMARK 470 LYS A 10 CG CD CE NZ REMARK 470 GLN A 11 CG CD OE1 NE2 REMARK 470 GLU A 14 CG CD OE1 OE2 REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 GLU A 60 CG CD OE1 OE2 REMARK 470 CYS A 69 SG REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 VAL A 71 CG1 CG2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 LYS A 129 CG CD CE NZ REMARK 470 LYS A 140 CG CD CE NZ REMARK 470 ASP A 262 CG OD1 OD2 REMARK 470 LYS A 269 CG CD CE NZ REMARK 470 GLU A 274 CG CD OE1 OE2 REMARK 470 LYS A 275 CG CD CE NZ REMARK 470 LYS A 300 CG CD CE NZ REMARK 470 ARG A 301 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 316 CG CD OE1 NE2 REMARK 470 GLU B 37 CG CD OE1 OE2 REMARK 470 LYS B 56 CG CD CE NZ REMARK 470 LYS B 59 CG CD CE NZ REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 VAL B 71 CG1 CG2 REMARK 470 GLN B 75 CG CD OE1 NE2 REMARK 470 LYS B 94 CG CD CE NZ REMARK 470 ASN B 95 CG OD1 ND2 REMARK 470 LEU B 97 CG CD1 CD2 REMARK 470 LYS B 119 CG CD CE NZ REMARK 470 LYS B 128 CG CD CE NZ REMARK 470 LYS B 140 CG CD CE NZ REMARK 470 GLU B 144 CG CD OE1 OE2 REMARK 470 ASP B 163 CG OD1 OD2 REMARK 470 PHE B 166 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU B 200 CG CD1 CD2 REMARK 470 LEU B 263 CG CD1 CD2 REMARK 470 LYS B 269 CG CD CE NZ REMARK 470 MET B 272 CG SD CE REMARK 470 ILE B 298 CG1 CG2 CD1 REMARK 470 LYS B 300 CG CD CE NZ REMARK 470 ARG B 301 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 302 CG1 CG2 REMARK 470 ARG B 336 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 337 CG CD1 CD2 CE1 CE2 CZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2 DC C 6 H22 DG D 12 1.56 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 DC C 6 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT C 7 O4' - C1' - N1 ANGL. DEV. = 2.1 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 GLU A 37 172.48 -55.40 REMARK 500 PRO A 39 90.02 -65.82 REMARK 500 SER A 57 58.97 -97.72 REMARK 500 ASP A 61 73.19 -57.00 REMARK 500 LEU A 96 70.67 49.91 REMARK 500 ASN A 106 -2.06 78.32 REMARK 500 SER A 160 31.86 -140.88 REMARK 500 GLN A 173 79.56 -117.28 REMARK 500 ASP A 181 -179.82 -170.37 REMARK 500 LEU A 199 72.74 -68.93 REMARK 500 TYR A 284 67.71 -104.45 REMARK 500 LYS A 300 -161.38 -69.47 REMARK 500 THR A 307 171.30 -58.51 REMARK 500 ASN A 334 75.02 -113.75 REMARK 500 THR A 340 39.83 -140.20 REMARK 500 CYS A 346 102.71 -168.54 REMARK 500 TRP B 42 104.39 -168.14 REMARK 500 ASP B 61 68.20 -60.17 REMARK 500 LYS B 70 37.18 -84.87 REMARK 500 ARG B 93 -22.40 78.14 REMARK 500 GLU B 116 122.85 -179.07 REMARK 500 ASP B 126 85.59 -60.33 REMARK 500 SER B 160 30.71 -153.13 REMARK 500 PHE B 166 64.26 -119.31 REMARK 500 GLN B 173 78.11 -115.13 REMARK 500 LEU B 263 46.32 -104.16 REMARK 500 LYS B 275 60.80 -105.39 REMARK 500 LYS B 294 61.82 64.85 REMARK 500 VAL B 302 -170.37 -65.10 REMARK 500 ALA B 303 142.46 178.83 REMARK 500 CYS B 346 115.92 -160.34 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 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 114 OD1 REMARK 620 2 ASP A 114 OD2 53.8 REMARK 620 3 GLU A 116 OE2 120.4 116.2 REMARK 620 4 DTP A 401 O2G 141.7 159.4 70.7 REMARK 620 5 DTP A 401 O2B 94.9 101.3 138.8 68.3 REMARK 620 6 DTP A 401 O2A 143.6 93.9 86.7 66.5 73.7 REMARK 620 7 HOH A 503 O 61.8 115.4 99.1 80.7 78.2 142.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 114 OD1 REMARK 620 2 ASP B 114 OD2 53.5 REMARK 620 3 GLU B 116 OE2 80.3 87.1 REMARK 620 4 DTP B 401 O2G 118.3 164.0 77.6 REMARK 620 5 DTP B 401 O2B 85.1 110.9 142.9 79.8 REMARK 620 6 DTP B 401 O2A 148.4 95.9 108.6 93.3 101.7 REMARK 620 7 HOH B 501 O 59.3 109.1 61.3 59.4 81.9 151.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 114 OD2 REMARK 620 2 GLU B 116 OE1 122.9 REMARK 620 3 GLU B 116 OE2 77.1 48.6 REMARK 620 4 ASP B 280 OD2 83.1 109.1 122.1 REMARK 620 5 DTP B 401 O2A 84.9 101.1 82.1 149.3 REMARK 620 N 1 2 3 4 DBREF 7JKP A 1 354 UNP Q96LW4 PRIPO_HUMAN 1 354 DBREF 7JKP C 1 17 PDB 7JKP 7JKP 1 17 DBREF 7JKP D 2 14 PDB 7JKP 7JKP 2 14 DBREF 7JKP B 1 354 UNP Q96LW4 PRIPO_HUMAN 1 354 DBREF 7JKP G 1 17 PDB 7JKP 7JKP 1 17 DBREF 7JKP H 2 14 PDB 7JKP 7JKP 2 14 SEQRES 1 A 354 MET ASN ARG LYS TRP GLU ALA LYS LEU LYS GLN ILE GLU SEQRES 2 A 354 GLU ARG ALA SER HIS TYR GLU ARG LYS PRO LEU SER SER SEQRES 3 A 354 VAL TYR ARG PRO ARG LEU SER LYS PRO GLU GLU PRO PRO SEQRES 4 A 354 SER ILE TRP ARG LEU PHE HIS ARG GLN ALA GLN ALA PHE SEQRES 5 A 354 ASN PHE VAL LYS SER CYS LYS GLU ASP VAL HIS VAL PHE SEQRES 6 A 354 ALA LEU GLU CYS LYS VAL GLY ASP GLY GLN ARG ILE TYR SEQRES 7 A 354 LEU VAL THR THR TYR ALA GLU PHE TRP PHE TYR TYR LYS SEQRES 8 A 354 SER ARG LYS ASN LEU LEU HIS CYS TYR GLU VAL ILE PRO SEQRES 9 A 354 GLU ASN ALA VAL CYS LYS LEU TYR PHE ASP LEU GLU PHE SEQRES 10 A 354 ASN LYS PRO ALA ASN PRO GLY ALA ASP GLY LYS LYS MET SEQRES 11 A 354 VAL ALA LEU LEU ILE GLU TYR VAL CYS LYS ALA LEU GLN SEQRES 12 A 354 GLU LEU TYR GLY VAL ASN CYS SER ALA GLU ASP VAL LEU SEQRES 13 A 354 ASN LEU ASP SER SER THR ASP GLU LYS PHE SER ARG HIS SEQRES 14 A 354 LEU ILE PHE GLN LEU HIS ASP VAL ALA PHE LYS ASP ASN SEQRES 15 A 354 ILE HIS VAL GLY ASN PHE LEU ARG LYS ILE LEU GLN PRO SEQRES 16 A 354 ALA LEU ASP LEU LEU GLY SER GLU ASP ASP ASP SER ALA SEQRES 17 A 354 PRO GLU THR THR GLY HIS GLY PHE PRO HIS PHE SER GLU SEQRES 18 A 354 ALA PRO ALA ARG GLN GLY PHE SER PHE ASN LYS MET PHE SEQRES 19 A 354 THR GLU LYS ALA THR GLU GLU SER TRP THR SER ASN SER SEQRES 20 A 354 LYS LYS LEU GLU ARG LEU GLY SER ALA GLU GLN SER SER SEQRES 21 A 354 PRO ASP LEU SER PHE LEU VAL VAL LYS ASN ASN MET GLY SEQRES 22 A 354 GLU LYS HIS LEU PHE VAL ASP LEU GLY VAL TYR THR ARG SEQRES 23 A 354 ASN ARG ASN PHE ARG LEU TYR LYS SER SER LYS ILE GLY SEQRES 24 A 354 LYS ARG VAL ALA LEU GLU VAL THR GLU ASP ASN LYS PHE SEQRES 25 A 354 PHE PRO ILE GLN SER LYS ASP VAL SER ASP GLU TYR GLN SEQRES 26 A 354 TYR PHE LEU SER SER LEU VAL SER ASN VAL ARG PHE SER SEQRES 27 A 354 ASP THR LEU ARG ILE LEU THR CYS GLU PRO SER GLN ASN SEQRES 28 A 354 LYS GLN LYS SEQRES 1 C 17 DC DA 8OG DC DG DC DT DA DC DC DA DC DA SEQRES 2 C 17 DC DC DC DC SEQRES 1 D 13 DG DG DG DT DG DT DG DG DT DA DG DC DG SEQRES 1 B 354 MET ASN ARG LYS TRP GLU ALA LYS LEU LYS GLN ILE GLU SEQRES 2 B 354 GLU ARG ALA SER HIS TYR GLU ARG LYS PRO LEU SER SER SEQRES 3 B 354 VAL TYR ARG PRO ARG LEU SER LYS PRO GLU GLU PRO PRO SEQRES 4 B 354 SER ILE TRP ARG LEU PHE HIS ARG GLN ALA GLN ALA PHE SEQRES 5 B 354 ASN PHE VAL LYS SER CYS LYS GLU ASP VAL HIS VAL PHE SEQRES 6 B 354 ALA LEU GLU CYS LYS VAL GLY ASP GLY GLN ARG ILE TYR SEQRES 7 B 354 LEU VAL THR THR TYR ALA GLU PHE TRP PHE TYR TYR LYS SEQRES 8 B 354 SER ARG LYS ASN LEU LEU HIS CYS TYR GLU VAL ILE PRO SEQRES 9 B 354 GLU ASN ALA VAL CYS LYS LEU TYR PHE ASP LEU GLU PHE SEQRES 10 B 354 ASN LYS PRO ALA ASN PRO GLY ALA ASP GLY LYS LYS MET SEQRES 11 B 354 VAL ALA LEU LEU ILE GLU TYR VAL CYS LYS ALA LEU GLN SEQRES 12 B 354 GLU LEU TYR GLY VAL ASN CYS SER ALA GLU ASP VAL LEU SEQRES 13 B 354 ASN LEU ASP SER SER THR ASP GLU LYS PHE SER ARG HIS SEQRES 14 B 354 LEU ILE PHE GLN LEU HIS ASP VAL ALA PHE LYS ASP ASN SEQRES 15 B 354 ILE HIS VAL GLY ASN PHE LEU ARG LYS ILE LEU GLN PRO SEQRES 16 B 354 ALA LEU ASP LEU LEU GLY SER GLU ASP ASP ASP SER ALA SEQRES 17 B 354 PRO GLU THR THR GLY HIS GLY PHE PRO HIS PHE SER GLU SEQRES 18 B 354 ALA PRO ALA ARG GLN GLY PHE SER PHE ASN LYS MET PHE SEQRES 19 B 354 THR GLU LYS ALA THR GLU GLU SER TRP THR SER ASN SER SEQRES 20 B 354 LYS LYS LEU GLU ARG LEU GLY SER ALA GLU GLN SER SER SEQRES 21 B 354 PRO ASP LEU SER PHE LEU VAL VAL LYS ASN ASN MET GLY SEQRES 22 B 354 GLU LYS HIS LEU PHE VAL ASP LEU GLY VAL TYR THR ARG SEQRES 23 B 354 ASN ARG ASN PHE ARG LEU TYR LYS SER SER LYS ILE GLY SEQRES 24 B 354 LYS ARG VAL ALA LEU GLU VAL THR GLU ASP ASN LYS PHE SEQRES 25 B 354 PHE PRO ILE GLN SER LYS ASP VAL SER ASP GLU TYR GLN SEQRES 26 B 354 TYR PHE LEU SER SER LEU VAL SER ASN VAL ARG PHE SER SEQRES 27 B 354 ASP THR LEU ARG ILE LEU THR CYS GLU PRO SER GLN ASN SEQRES 28 B 354 LYS GLN LYS SEQRES 1 G 17 DC DA 8OG DC DG DC DT DA DC DC DA DC DA SEQRES 2 G 17 DC DC DC DC SEQRES 1 H 13 DG DG DG DT DG DT DG DG DT DA DG DC DG HET 8OG C 3 34 HET 8OG G 3 34 HET DTP A 401 42 HET CA A 402 1 HET GOL A 403 14 HET DTP B 401 42 HET CA B 402 1 HET CA B 403 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 8OG 2(C10 H14 N5 O8 P) FORMUL 7 DTP 2(C10 H16 N5 O12 P3) FORMUL 8 CA 3(CA 2+) FORMUL 9 GOL C3 H8 O3 FORMUL 13 HOH *24(H2 O) HELIX 1 AA1 MET A 1 GLU A 14 1 14 HELIX 2 AA2 ARG A 47 SER A 57 1 11 HELIX 3 AA3 THR A 82 TYR A 89 1 8 HELIX 4 AA4 ASP A 126 GLY A 147 1 22 HELIX 5 AA5 SER A 151 GLU A 153 5 3 HELIX 6 AA6 ASP A 181 LEU A 193 1 13 HELIX 7 AA7 LEU A 193 LEU A 199 1 7 HELIX 8 AA8 LEU A 263 PHE A 265 5 3 HELIX 9 AA9 SER A 321 LEU A 331 1 11 HELIX 10 AB1 ARG B 47 LYS B 59 1 13 HELIX 11 AB2 THR B 82 LYS B 91 1 10 HELIX 12 AB3 ASP B 126 GLY B 147 1 22 HELIX 13 AB4 SER B 151 GLU B 153 5 3 HELIX 14 AB5 ASP B 181 LEU B 193 1 13 HELIX 15 AB6 LEU B 193 LEU B 200 1 8 HELIX 16 AB7 LEU B 263 VAL B 267 5 5 HELIX 17 AB8 SER B 321 LEU B 331 1 11 SHEET 1 AA1 5 ARG A 43 PHE A 45 0 SHEET 2 AA1 5 ARG A 76 THR A 81 -1 O TYR A 78 N PHE A 45 SHEET 3 AA1 5 HIS A 63 GLU A 68 -1 N LEU A 67 O ILE A 77 SHEET 4 AA1 5 CYS A 99 ILE A 103 -1 O TYR A 100 N ALA A 66 SHEET 5 AA1 5 ARG A 288 ARG A 291 -1 O PHE A 290 N GLU A 101 SHEET 1 AA2 4 TYR A 112 ASN A 118 0 SHEET 2 AA2 4 LYS A 165 PHE A 172 -1 O ARG A 168 N LEU A 115 SHEET 3 AA2 4 VAL A 155 ASP A 159 -1 N LEU A 156 O ILE A 171 SHEET 4 AA2 4 GLU A 305 VAL A 306 -1 O GLU A 305 N ASP A 159 SHEET 1 AA3 4 VAL A 177 PHE A 179 0 SHEET 2 AA3 4 ARG A 342 LEU A 344 1 O LEU A 344 N ALA A 178 SHEET 3 AA3 4 ARG B 342 LEU B 344 -1 O ILE B 343 N ILE A 343 SHEET 4 AA3 4 VAL B 177 PHE B 179 1 N ALA B 178 O LEU B 344 SHEET 1 AA4 2 VAL A 267 LYS A 269 0 SHEET 2 AA4 2 LYS A 275 LEU A 277 -1 O HIS A 276 N VAL A 268 SHEET 1 AA5 5 ARG B 43 PHE B 45 0 SHEET 2 AA5 5 ARG B 76 THR B 81 -1 O TYR B 78 N PHE B 45 SHEET 3 AA5 5 HIS B 63 GLU B 68 -1 N LEU B 67 O ILE B 77 SHEET 4 AA5 5 CYS B 99 ILE B 103 -1 O TYR B 100 N ALA B 66 SHEET 5 AA5 5 ARG B 288 ARG B 291 -1 O ARG B 288 N ILE B 103 SHEET 1 AA6 4 TYR B 112 LEU B 115 0 SHEET 2 AA6 4 ARG B 168 PHE B 172 -1 O ARG B 168 N LEU B 115 SHEET 3 AA6 4 VAL B 155 ASP B 159 -1 N LEU B 156 O ILE B 171 SHEET 4 AA6 4 GLU B 305 VAL B 306 -1 O GLU B 305 N ASP B 159 LINK O3' DA C 2 P 8OG C 3 1555 1555 1.61 LINK O3' 8OG C 3 P DC C 4 1555 1555 1.61 LINK O3' DA G 2 P 8OG G 3 1555 1555 1.61 LINK O3' 8OG G 3 P DC G 4 1555 1555 1.61 LINK OD1 ASP A 114 CA CA A 402 1555 1555 2.38 LINK OD2 ASP A 114 CA CA A 402 1555 1555 2.47 LINK OE2 GLU A 116 CA CA A 402 1555 1555 2.32 LINK O2G DTP A 401 CA CA A 402 1555 1555 2.11 LINK O2B DTP A 401 CA CA A 402 1555 1555 2.34 LINK O2A DTP A 401 CA CA A 402 1555 1555 2.12 LINK CA CA A 402 O HOH A 503 1555 1555 2.31 LINK OD1 ASP B 114 CA CA B 402 1555 1555 2.44 LINK OD2 ASP B 114 CA CA B 402 1555 1555 2.43 LINK OD2 ASP B 114 CA CA B 403 1555 1555 2.38 LINK OE2 GLU B 116 CA CA B 402 1555 1555 2.30 LINK OE1 GLU B 116 CA CA B 403 1555 1555 2.42 LINK OE2 GLU B 116 CA CA B 403 1555 1555 2.83 LINK OD2 ASP B 280 CA CA B 403 1555 1555 2.47 LINK O2G DTP B 401 CA CA B 402 1555 1555 2.28 LINK O2B DTP B 401 CA CA B 402 1555 1555 1.90 LINK O2A DTP B 401 CA CA B 402 1555 1555 2.09 LINK O2A DTP B 401 CA CA B 403 1555 1555 2.60 LINK CA CA B 402 O HOH B 501 1555 1555 2.47 CRYST1 52.225 65.656 74.482 69.30 82.87 88.06 P 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 0.019148 -0.000647 -0.002314 0.00000 SCALE2 0.000000 0.015240 -0.005736 0.00000 SCALE3 0.000000 0.000000 0.014457 0.00000