HEADER TRANSFERASE/DNA 06-JAN-11 3Q8P TITLE HUMAN DNA POLYMERASE IOTA INCORPORATING DCTP OPPOSITE 8-OXO-GUANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IOTA; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: UNP RESIDUES 1-420; COMPND 5 SYNONYM: ETA2, RAD30 HOMOLOG B; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*TP*CP*AP*(8OG)P*GP*GP*GP*TP*CP*CP*T)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3'); COMPND 14 CHAIN: P; 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: POLI, RAD30B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.N.KIROUAC,H.LING REVDAT 3 21-FEB-24 3Q8P 1 REMARK LINK REVDAT 2 30-MAR-11 3Q8P 1 JRNL REVDAT 1 23-FEB-11 3Q8P 0 JRNL AUTH K.N.KIROUAC,H.LING JRNL TITL UNIQUE ACTIVE SITE PROMOTES ERROR-FREE REPLICATION OPPOSITE JRNL TITL 2 AN 8-OXO-GUANINE LESION BY HUMAN DNA POLYMERASE IOTA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 3210 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21300901 JRNL DOI 10.1073/PNAS.1013909108 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 41545 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.510 REMARK 3 FREE R VALUE TEST SET COUNT : 1457 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 32.7382 - 4.1995 0.96 4345 158 0.2090 0.2491 REMARK 3 2 4.1995 - 3.3344 0.99 4243 154 0.2033 0.2293 REMARK 3 3 3.3344 - 2.9132 0.99 4168 153 0.2341 0.2326 REMARK 3 4 2.9132 - 2.6469 0.99 4154 153 0.2425 0.2966 REMARK 3 5 2.6469 - 2.4573 0.98 4095 148 0.2449 0.2805 REMARK 3 6 2.4573 - 2.3125 0.97 4043 145 0.2317 0.2989 REMARK 3 7 2.3125 - 2.1967 0.96 3986 146 0.2382 0.2842 REMARK 3 8 2.1967 - 2.1011 0.94 3897 144 0.2281 0.2487 REMARK 3 9 2.1011 - 2.0202 0.91 3714 133 0.2642 0.2853 REMARK 3 10 2.0202 - 1.9500 0.83 3443 123 0.3016 0.3423 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 48.80 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.17220 REMARK 3 B22 (A**2) : 3.17220 REMARK 3 B33 (A**2) : -6.34450 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 : 0.006 3450 REMARK 3 ANGLE : 1.266 4742 REMARK 3 CHIRALITY : 0.085 548 REMARK 3 PLANARITY : 0.003 547 REMARK 3 DIHEDRAL : 20.119 1336 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN B AND RESID 27:97) REMARK 3 ORIGIN FOR THE GROUP (A): -1.6655 -16.4831 -21.0409 REMARK 3 T TENSOR REMARK 3 T11: 0.0468 T22: 0.0707 REMARK 3 T33: 0.4265 T12: 0.1205 REMARK 3 T13: -0.0999 T23: -0.1508 REMARK 3 L TENSOR REMARK 3 L11: 0.7671 L22: 3.8759 REMARK 3 L33: 1.1947 L12: 0.0936 REMARK 3 L13: 0.1407 L23: 0.8241 REMARK 3 S TENSOR REMARK 3 S11: -0.0370 S12: -0.1160 S13: 0.0656 REMARK 3 S21: -0.3092 S22: -0.4076 S23: 1.2292 REMARK 3 S31: -0.3262 S32: -0.1701 S33: 0.4427 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESID 98:148) REMARK 3 ORIGIN FOR THE GROUP (A): 20.4298 -19.5881 -12.7167 REMARK 3 T TENSOR REMARK 3 T11: 0.1283 T22: 0.1614 REMARK 3 T33: 0.0980 T12: 0.0207 REMARK 3 T13: 0.0342 T23: 0.0303 REMARK 3 L TENSOR REMARK 3 L11: 0.9960 L22: 0.6188 REMARK 3 L33: 1.2432 L12: -0.5295 REMARK 3 L13: -0.7045 L23: 0.4165 REMARK 3 S TENSOR REMARK 3 S11: 0.0070 S12: -0.0602 S13: -0.0134 REMARK 3 S21: -0.0291 S22: -0.0382 S23: -0.0044 REMARK 3 S31: 0.0138 S32: 0.3042 S33: -0.0202 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN B AND RESID 149:190) REMARK 3 ORIGIN FOR THE GROUP (A): 17.5546 -11.1529 -0.6663 REMARK 3 T TENSOR REMARK 3 T11: 0.1846 T22: 0.1388 REMARK 3 T33: 0.0880 T12: -0.0480 REMARK 3 T13: 0.0286 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 0.4783 L22: 0.5022 REMARK 3 L33: 0.3221 L12: -0.2269 REMARK 3 L13: 0.0757 L23: 0.3160 REMARK 3 S TENSOR REMARK 3 S11: 0.0369 S12: -0.1361 S13: 0.1083 REMARK 3 S21: 0.1323 S22: -0.0472 S23: -0.0353 REMARK 3 S31: 0.0014 S32: 0.0825 S33: -0.0060 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 191:299) REMARK 3 ORIGIN FOR THE GROUP (A): 5.7733 -29.5530 -0.5899 REMARK 3 T TENSOR REMARK 3 T11: 0.1522 T22: 0.0832 REMARK 3 T33: 0.1364 T12: 0.0097 REMARK 3 T13: 0.0757 T23: -0.0136 REMARK 3 L TENSOR REMARK 3 L11: 0.9222 L22: -0.0112 REMARK 3 L33: 1.5713 L12: 0.0402 REMARK 3 L13: -0.8917 L23: -0.1054 REMARK 3 S TENSOR REMARK 3 S11: -0.1383 S12: 0.0014 S13: -0.1996 REMARK 3 S21: 0.0895 S22: -0.0820 S23: 0.0501 REMARK 3 S31: 0.1308 S32: 0.0610 S33: 0.1889 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 300:414) REMARK 3 ORIGIN FOR THE GROUP (A): 7.1968 -42.1081 -34.5674 REMARK 3 T TENSOR REMARK 3 T11: 0.6754 T22: 0.3554 REMARK 3 T33: 0.3921 T12: 0.1886 REMARK 3 T13: -0.2095 T23: -0.1786 REMARK 3 L TENSOR REMARK 3 L11: 0.9944 L22: 5.0638 REMARK 3 L33: 1.0096 L12: -0.8227 REMARK 3 L13: 0.5866 L23: 0.6747 REMARK 3 S TENSOR REMARK 3 S11: 0.4437 S12: 0.2995 S13: -0.1404 REMARK 3 S21: -1.3470 S22: -0.2597 S23: 0.7458 REMARK 3 S31: 0.0733 S32: 0.2294 S33: -0.0827 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 3Q8P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063334. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41545 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 5000MME, 0.15M NH4SO4, 0.1M REMARK 280 MES PH 6.5, 2.5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 134.87867 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 67.43933 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 101.15900 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 33.71967 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 168.59833 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 134.87867 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 67.43933 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 33.71967 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 101.15900 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 168.59833 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, T, P 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 B 1 REMARK 465 GLU B 2 REMARK 465 LEU B 3 REMARK 465 ALA B 4 REMARK 465 ASP B 5 REMARK 465 VAL B 6 REMARK 465 GLY B 7 REMARK 465 ALA B 8 REMARK 465 ALA B 9 REMARK 465 ALA B 10 REMARK 465 SER B 11 REMARK 465 SER B 12 REMARK 465 GLN B 13 REMARK 465 GLY B 14 REMARK 465 VAL B 15 REMARK 465 HIS B 16 REMARK 465 ASP B 17 REMARK 465 GLN B 18 REMARK 465 VAL B 19 REMARK 465 LEU B 20 REMARK 465 PRO B 21 REMARK 465 THR B 22 REMARK 465 PRO B 23 REMARK 465 ASN B 24 REMARK 465 ALA B 25 REMARK 465 SER B 26 REMARK 465 SER B 351 REMARK 465 GLU B 352 REMARK 465 LYS B 353 REMARK 465 HIS B 354 REMARK 465 TYR B 355 REMARK 465 GLY B 373 REMARK 465 THR B 374 REMARK 465 GLY B 375 REMARK 465 ALA B 415 REMARK 465 LEU B 416 REMARK 465 ASN B 417 REMARK 465 THR B 418 REMARK 465 ALA B 419 REMARK 465 LYS B 420 REMARK 465 DT T 837 REMARK 465 DC T 838 REMARK 465 DA T 839 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 SER B 27 OG REMARK 470 GLU B 49 CG CD OE1 OE2 REMARK 470 LYS B 85 CG CD CE NZ REMARK 470 GLU B 86 CG CD OE1 OE2 REMARK 470 GLN B 144 CG CD OE1 NE2 REMARK 470 SER B 145 OG REMARK 470 ASP B 146 CG OD1 OD2 REMARK 470 LYS B 237 CG CD CE NZ REMARK 470 LYS B 248 CG CD CE NZ REMARK 470 LYS B 267 CG CD CE NZ REMARK 470 GLU B 272 CG CD OE1 OE2 REMARK 470 LEU B 372 CG CD1 CD2 REMARK 470 ASN B 376 CG OD1 ND2 REMARK 470 TYR B 377 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 DC P 873 O3' 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 O2A DCP B 421 O HOH B 436 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 O3' DT T 847 P DA P 867 12544 2.06 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 DG T 841 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG T 842 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG T 843 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 DG T 843 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT T 847 O4' - C1' - N1 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA P 870 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC P 873 O4' - C1' - N1 ANGL. DEV. = 2.0 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 CYS B 37 66.06 30.99 REMARK 500 PRO B 48 -8.12 -56.82 REMARK 500 LYS B 51 8.84 -69.61 REMARK 500 LYS B 60 -113.42 57.62 REMARK 500 CYS B 88 75.88 -166.76 REMARK 500 GLN B 144 -159.21 -96.36 REMARK 500 ALA B 150 -43.30 133.02 REMARK 500 ASP B 289 103.19 -161.59 REMARK 500 ASP B 289 103.49 -161.59 REMARK 500 LYS B 371 -49.80 -131.94 REMARK 500 TYR B 377 -156.90 -107.05 REMARK 500 PHE B 401 -168.02 -162.37 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 MG B 423 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 34 OD1 REMARK 620 2 LEU B 35 O 99.2 REMARK 620 3 ASP B 126 OD1 90.6 93.1 REMARK 620 4 DCP B 421 O2B 154.0 106.8 87.9 REMARK 620 5 DCP B 421 O2G 92.3 94.1 171.6 85.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 422 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 237 O REMARK 620 2 ILE B 239 O 91.3 REMARK 620 3 ILE B 242 O 87.4 83.7 REMARK 620 4 HOH B 615 O 83.0 85.7 165.5 REMARK 620 5 HOH P 176 O 95.4 171.6 91.5 100.2 REMARK 620 6 DC P 872 OP1 176.7 90.3 89.9 100.0 82.8 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 DCP B 421 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 423 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3Q8S RELATED DB: PDB REMARK 900 RELATED ID: 3Q8Q RELATED DB: PDB REMARK 900 RELATED ID: 3Q8R RELATED DB: PDB DBREF 3Q8P B 1 420 UNP Q9UNA4 POLI_HUMAN 1 420 DBREF 3Q8P T 837 847 PDB 3Q8P 3Q8P 837 847 DBREF 3Q8P P 867 873 PDB 3Q8P 3Q8P 867 873 SEQRES 1 B 420 MET GLU LEU ALA ASP VAL GLY ALA ALA ALA SER SER GLN SEQRES 2 B 420 GLY VAL HIS ASP GLN VAL LEU PRO THR PRO ASN ALA SER SEQRES 3 B 420 SER ARG VAL ILE VAL HIS VAL ASP LEU ASP CYS PHE TYR SEQRES 4 B 420 ALA GLN VAL GLU MET ILE SER ASN PRO GLU LEU LYS ASP SEQRES 5 B 420 LYS PRO LEU GLY VAL GLN GLN LYS TYR LEU VAL VAL THR SEQRES 6 B 420 CYS ASN TYR GLU ALA ARG LYS LEU GLY VAL LYS LYS LEU SEQRES 7 B 420 MET ASN VAL ARG ASP ALA LYS GLU LYS CYS PRO GLN LEU SEQRES 8 B 420 VAL LEU VAL ASN GLY GLU ASP LEU THR ARG TYR ARG GLU SEQRES 9 B 420 MET SER TYR LYS VAL THR GLU LEU LEU GLU GLU PHE SER SEQRES 10 B 420 PRO VAL VAL GLU ARG LEU GLY PHE ASP GLU ASN PHE VAL SEQRES 11 B 420 ASP LEU THR GLU MET VAL GLU LYS ARG LEU GLN GLN LEU SEQRES 12 B 420 GLN SER ASP GLU LEU SER ALA VAL THR VAL SER GLY HIS SEQRES 13 B 420 VAL TYR ASN ASN GLN SER ILE ASN LEU LEU ASP VAL LEU SEQRES 14 B 420 HIS ILE ARG LEU LEU VAL GLY SER GLN ILE ALA ALA GLU SEQRES 15 B 420 MET ARG GLU ALA MET TYR ASN GLN LEU GLY LEU THR GLY SEQRES 16 B 420 CYS ALA GLY VAL ALA SER ASN LYS LEU LEU ALA LYS LEU SEQRES 17 B 420 VAL SER GLY VAL PHE LYS PRO ASN GLN GLN THR VAL LEU SEQRES 18 B 420 LEU PRO GLU SER CYS GLN HIS LEU ILE HIS SER LEU ASN SEQRES 19 B 420 HIS ILE LYS GLU ILE PRO GLY ILE GLY TYR LYS THR ALA SEQRES 20 B 420 LYS CYS LEU GLU ALA LEU GLY ILE ASN SER VAL ARG ASP SEQRES 21 B 420 LEU GLN THR PHE SER PRO LYS ILE LEU GLU LYS GLU LEU SEQRES 22 B 420 GLY ILE SER VAL ALA GLN ARG ILE GLN LYS LEU SER PHE SEQRES 23 B 420 GLY GLU ASP ASN SER PRO VAL ILE LEU SER GLY PRO PRO SEQRES 24 B 420 GLN SER PHE SER GLU GLU ASP SER PHE LYS LYS CYS SER SEQRES 25 B 420 SER GLU VAL GLU ALA LYS ASN LYS ILE GLU GLU LEU LEU SEQRES 26 B 420 ALA SER LEU LEU ASN ARG VAL CYS GLN ASP GLY ARG LYS SEQRES 27 B 420 PRO HIS THR VAL ARG LEU ILE ILE ARG ARG TYR SER SER SEQRES 28 B 420 GLU LYS HIS TYR GLY ARG GLU SER ARG GLN CYS PRO ILE SEQRES 29 B 420 PRO SER HIS VAL ILE GLN LYS LEU GLY THR GLY ASN TYR SEQRES 30 B 420 ASP VAL MET THR PRO MET VAL ASP ILE LEU MET LYS LEU SEQRES 31 B 420 PHE ARG ASN MET VAL ASN VAL LYS MET PRO PHE HIS LEU SEQRES 32 B 420 THR LEU LEU SER VAL CYS PHE CYS ASN LEU LYS ALA LEU SEQRES 33 B 420 ASN THR ALA LYS SEQRES 1 T 11 DT DC DA 8OG DG DG DG DT DC DC DT SEQRES 1 P 7 DA DG DG DA DC DC DC MODRES 3Q8P 8OG T 840 DG HET 8OG T 840 46 HET DCP B 421 28 HET MG B 422 1 HET MG B 423 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 4 DCP C9 H16 N3 O13 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *398(H2 O) HELIX 1 1 CYS B 37 ASN B 47 1 11 HELIX 2 2 ASN B 67 LEU B 73 1 7 HELIX 3 3 VAL B 81 CYS B 88 1 8 HELIX 4 4 LEU B 99 SER B 117 1 19 HELIX 5 5 LEU B 132 LEU B 143 1 12 HELIX 6 6 SER B 145 SER B 149 5 5 HELIX 7 7 ASN B 159 GLN B 161 5 3 HELIX 8 8 ASP B 167 GLY B 192 1 26 HELIX 9 9 ASN B 202 GLY B 211 1 10 HELIX 10 10 LEU B 222 GLU B 224 5 3 HELIX 11 11 SER B 225 LEU B 233 1 9 HELIX 12 12 HIS B 235 ILE B 239 5 5 HELIX 13 13 GLY B 243 LEU B 253 1 11 HELIX 14 14 SER B 257 PHE B 264 1 8 HELIX 15 15 SER B 265 GLY B 274 1 10 HELIX 16 16 GLY B 274 PHE B 286 1 13 HELIX 17 17 SER B 313 GLY B 336 1 24 HELIX 18 18 PRO B 365 GLN B 370 1 6 HELIX 19 19 VAL B 379 VAL B 395 1 17 SHEET 1 A 6 VAL B 120 LEU B 123 0 SHEET 2 A 6 GLU B 127 ASP B 131 -1 O PHE B 129 N GLU B 121 SHEET 3 A 6 ILE B 30 LEU B 35 -1 N VAL B 33 O ASN B 128 SHEET 4 A 6 GLY B 195 ALA B 200 -1 O ALA B 200 N ILE B 30 SHEET 5 A 6 GLN B 218 VAL B 220 1 O THR B 219 N VAL B 199 SHEET 6 A 6 HIS B 156 VAL B 157 1 N HIS B 156 O GLN B 218 SHEET 1 B 4 MET B 79 ASN B 80 0 SHEET 2 B 4 LEU B 62 CYS B 66 -1 N VAL B 63 O MET B 79 SHEET 3 B 4 LEU B 55 GLN B 59 -1 N VAL B 57 O THR B 65 SHEET 4 B 4 VAL B 92 ASN B 95 1 O VAL B 94 N GLN B 58 SHEET 1 C 4 SER B 301 CYS B 311 0 SHEET 2 C 4 LEU B 403 LEU B 413 -1 O PHE B 410 N PHE B 302 SHEET 3 C 4 PRO B 339 ARG B 348 -1 N ARG B 347 O THR B 404 SHEET 4 C 4 ARG B 357 PRO B 363 -1 O ARG B 360 N LEU B 344 LINK O3'A8OG T 840 P DG T 841 1555 1555 1.59 LINK O3'B8OG T 840 P DG T 841 1555 1555 1.61 LINK OD1 ASP B 34 MG MG B 423 1555 1555 2.27 LINK O LEU B 35 MG MG B 423 1555 1555 2.09 LINK OD1 ASP B 126 MG MG B 423 1555 1555 2.16 LINK O LYS B 237 MG MG B 422 1555 1555 2.47 LINK O ILE B 239 MG MG B 422 1555 1555 2.74 LINK O ILE B 242 MG MG B 422 1555 1555 2.51 LINK O2BADCP B 421 MG MG B 423 1555 1555 2.15 LINK O2GADCP B 421 MG MG B 423 1555 1555 2.20 LINK MG MG B 422 O HOH B 615 1555 1555 2.67 LINK MG MG B 422 O HOH P 176 1555 1555 2.58 LINK MG MG B 422 OP1 DC P 872 1555 1555 2.55 CISPEP 1 SER B 149 ALA B 150 0 2.65 CISPEP 2 LYS B 214 PRO B 215 0 -3.38 SITE 1 AC1 21 ASP B 34 LEU B 35 ASP B 36 CYS B 37 SITE 2 AC1 21 PHE B 38 THR B 65 TYR B 68 ARG B 71 SITE 3 AC1 21 LYS B 77 ASP B 126 LYS B 214 MG B 423 SITE 4 AC1 21 HOH B 436 HOH B 497 HOH B 551 HOH B 623 SITE 5 AC1 21 HOH B 632 HOH B 781 DC P 873 8OG T 840 SITE 6 AC1 21 DG T 841 SITE 1 AC2 6 LYS B 237 ILE B 239 ILE B 242 HOH B 615 SITE 2 AC2 6 HOH P 176 DC P 872 SITE 1 AC3 4 ASP B 34 LEU B 35 ASP B 126 DCP B 421 CRYST1 99.161 99.161 202.318 90.00 90.00 120.00 P 65 2 2 12 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 0.010085 0.005822 0.000000 0.00000 SCALE2 0.000000 0.011645 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004943 0.00000