PDB Short entry for 3Q8Q HEADER TRANSFERASE/DNA 06-JAN-11 3Q8Q TITLE HUMAN DNA POLYMERASE IOTA INCORPORATING DATP 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 3Q8Q 1 REMARK LINK REVDAT 2 30-MAR-11 3Q8Q 1 JRNL REVDAT 1 23-FEB-11 3Q8Q 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. 2.03 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 36888 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1292 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 32.6519 - 4.2220 0.99 4376 159 0.2036 0.2280 REMARK 3 2 4.2220 - 3.3522 0.99 4156 151 0.2100 0.2241 REMARK 3 3 3.3522 - 2.9288 0.99 4088 149 0.2354 0.2731 REMARK 3 4 2.9288 - 2.6611 0.98 4006 145 0.2472 0.2723 REMARK 3 5 2.6611 - 2.4705 0.97 3957 146 0.2560 0.2943 REMARK 3 6 2.4705 - 2.3249 0.96 3893 140 0.2476 0.2785 REMARK 3 7 2.3249 - 2.2085 0.94 3793 140 0.2590 0.2966 REMARK 3 8 2.2085 - 2.1123 0.92 3724 136 0.2459 0.2879 REMARK 3 9 2.1123 - 2.0310 0.89 3603 126 0.2847 0.3034 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 : 0.35 REMARK 3 B_SOL : 61.67 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.270 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) : 3.18380 REMARK 3 B22 (A**2) : 3.18380 REMARK 3 B33 (A**2) : -6.36760 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 3448 REMARK 3 ANGLE : 1.337 4743 REMARK 3 CHIRALITY : 0.090 548 REMARK 3 PLANARITY : 0.004 548 REMARK 3 DIHEDRAL : 20.948 1332 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN B AND RESID 28:105) REMARK 3 ORIGIN FOR THE GROUP (A): -0.3337 -16.9193 -22.3679 REMARK 3 T TENSOR REMARK 3 T11: 0.1707 T22: 0.1244 REMARK 3 T33: 0.1863 T12: 0.0896 REMARK 3 T13: -0.0765 T23: -0.1107 REMARK 3 L TENSOR REMARK 3 L11: 1.1967 L22: 1.9452 REMARK 3 L33: 1.4747 L12: -0.1530 REMARK 3 L13: 1.3310 L23: 0.3669 REMARK 3 S TENSOR REMARK 3 S11: -0.0724 S12: -0.1149 S13: -0.0102 REMARK 3 S21: -0.2987 S22: -0.2563 S23: 0.4179 REMARK 3 S31: -0.2594 S32: -0.0299 S33: 0.3222 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESID 106:223) REMARK 3 ORIGIN FOR THE GROUP (A): 17.5706 -15.5902 -4.8751 REMARK 3 T TENSOR REMARK 3 T11: 0.1446 T22: 0.1089 REMARK 3 T33: 0.0876 T12: -0.0128 REMARK 3 T13: 0.0251 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.3551 L22: 0.1626 REMARK 3 L33: 0.8734 L12: -0.1109 REMARK 3 L13: -0.0922 L23: 0.3646 REMARK 3 S TENSOR REMARK 3 S11: 0.0039 S12: -0.0187 S13: -0.0037 REMARK 3 S21: 0.0303 S22: -0.0396 S23: -0.0015 REMARK 3 S31: -0.0413 S32: 0.1070 S33: 0.0243 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN B AND RESID 224:299) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9322 -34.6085 1.2772 REMARK 3 T TENSOR REMARK 3 T11: 0.1652 T22: 0.0543 REMARK 3 T33: 0.1942 T12: 0.0136 REMARK 3 T13: 0.1143 T23: -0.0151 REMARK 3 L TENSOR REMARK 3 L11: 1.5916 L22: -0.0229 REMARK 3 L33: 1.6698 L12: 0.2783 REMARK 3 L13: -1.2511 L23: -0.0794 REMARK 3 S TENSOR REMARK 3 S11: -0.1587 S12: -0.0316 S13: -0.3852 REMARK 3 S21: 0.0157 S22: -0.2206 S23: 0.0681 REMARK 3 S31: 0.0476 S32: 0.0273 S33: 0.3439 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 300:414) REMARK 3 ORIGIN FOR THE GROUP (A): 7.3957 -41.9069 -34.5633 REMARK 3 T TENSOR REMARK 3 T11: 0.5079 T22: 0.3296 REMARK 3 T33: 0.3983 T12: 0.1644 REMARK 3 T13: -0.2036 T23: -0.2229 REMARK 3 L TENSOR REMARK 3 L11: 1.4470 L22: 4.4198 REMARK 3 L33: 1.1417 L12: -1.4562 REMARK 3 L13: 0.2900 L23: 0.4531 REMARK 3 S TENSOR REMARK 3 S11: 0.5325 S12: 0.1543 S13: -0.2703 REMARK 3 S21: -0.9402 S22: -0.2517 S23: 0.7239 REMARK 3 S31: 0.0740 S32: 0.1708 S33: -0.1894 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 3Q8Q 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_1000063335. 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 : 36888 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 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 (%) : 96.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 5000MME, 0.15M NH4SO4, 0.1M REMARK 280 MES 6.5, 2.5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K, PH 6.5 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 134.84733 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 67.42367 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 101.13550 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 33.71183 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 168.55917 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 134.84733 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 67.42367 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 33.71183 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 101.13550 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 168.55917 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: 4730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19290 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 LYS B 51 CG CD CE NZ REMARK 470 MET B 79 CG SD CE REMARK 470 ARG B 82 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 85 CG CD CE NZ REMARK 470 GLU B 86 CG CD OE1 OE2 REMARK 470 ASP B 146 CG OD1 OD2 REMARK 470 LYS B 248 CG CD CE NZ REMARK 470 LYS B 267 CG CD CE NZ REMARK 470 LYS B 271 CG CD CE NZ 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 LYS B 398 CG CD CE NZ REMARK 470 DC P 873 O3' 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 2.00 REMARK 500 OE1 GLN B 190 NH1 ARG B 259 6554 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 DT T 847 O3' DT T 847 C3' -0.037 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 ARG B 259 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG T 841 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG T 842 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG T 843 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES REMARK 500 DG T 843 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT T 844 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA P 870 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC P 873 O4' - C1' - N1 ANGL. DEV. = 2.9 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 63.26 31.43 REMARK 500 LYS B 60 -115.50 51.18 REMARK 500 CYS B 88 74.09 -153.00 REMARK 500 ALA B 150 -45.06 132.71 REMARK 500 LYS B 371 -52.05 -125.61 REMARK 500 TYR B 377 -153.44 -129.72 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 422 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 34 OD1 REMARK 620 2 LEU B 35 O 98.3 REMARK 620 3 DTP T 1 O1G 96.7 94.5 REMARK 620 4 DTP T 1 O2B 172.7 88.6 84.8 REMARK 620 5 DTP T 1 O2A 88.3 168.1 94.5 84.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 421 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 237 O REMARK 620 2 ILE B 239 O 85.2 REMARK 620 3 ILE B 242 O 84.0 82.1 REMARK 620 4 HOH B 445 O 86.4 80.7 160.9 REMARK 620 5 HOH B 553 O 96.4 173.5 91.7 105.7 REMARK 620 6 DC P 872 OP1 174.7 91.8 91.3 97.4 86.2 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 MG 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 DTP T 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3Q8P RELATED DB: PDB REMARK 900 RELATED ID: 3Q8S RELATED DB: PDB REMARK 900 RELATED ID: 3Q8R RELATED DB: PDB DBREF 3Q8Q B 1 420 UNP Q9UNA4 POLI_HUMAN 1 420 DBREF 3Q8Q T 837 847 PDB 3Q8Q 3Q8Q 837 847 DBREF 3Q8Q P 867 873 PDB 3Q8Q 3Q8Q 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 3Q8Q 8OG T 840 DG HET 8OG T 840 46 HET MG B 421 1 HET MG B 422 1 HET DTP T 1 30 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 4 MG 2(MG 2+) FORMUL 6 DTP C10 H16 N5 O12 P3 FORMUL 7 HOH *297(H2 O) HELIX 1 1 CYS B 37 ASN B 47 1 11 HELIX 2 2 PRO B 48 LYS B 51 5 4 HELIX 3 3 ASN B 67 LEU B 73 1 7 HELIX 4 4 VAL B 81 CYS B 88 1 8 HELIX 5 5 LEU B 99 SER B 117 1 19 HELIX 6 6 LEU B 132 LEU B 143 1 12 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 SER B 232 1 8 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 GLU B 127 N LEU B 123 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 1.60 LINK OD1 ASP B 34 MG MG B 422 1555 1555 2.34 LINK O LEU B 35 MG MG B 422 1555 1555 2.15 LINK O LYS B 237 MG MG B 421 1555 1555 2.54 LINK O ILE B 239 MG MG B 421 1555 1555 2.75 LINK O ILE B 242 MG MG B 421 1555 1555 2.57 LINK MG MG B 421 O HOH B 445 1555 1555 2.60 LINK MG MG B 421 O HOH B 553 1555 1555 2.55 LINK MG MG B 421 OP1 DC P 872 1555 1555 2.53 LINK MG MG B 422 O1G DTP T 1 1555 1555 2.41 LINK MG MG B 422 O2B DTP T 1 1555 1555 2.53 LINK MG MG B 422 O2A DTP T 1 1555 1555 2.62 CISPEP 1 SER B 149 ALA B 150 0 3.86 CISPEP 2 LYS B 214 PRO B 215 0 -5.71 SITE 1 AC1 6 LYS B 237 ILE B 239 ILE B 242 HOH B 445 SITE 2 AC1 6 HOH B 553 DC P 872 SITE 1 AC2 4 ASP B 34 LEU B 35 ASP B 126 DTP T 1 SITE 1 AC3 19 ASP B 34 LEU B 35 ASP B 36 CYS B 37 SITE 2 AC3 19 PHE B 38 VAL B 64 THR B 65 TYR B 68 SITE 3 AC3 19 ARG B 71 LYS B 77 ASP B 126 GLU B 127 SITE 4 AC3 19 LYS B 214 MG B 422 HOH B 569 DC P 873 SITE 5 AC3 19 HOH T 37 8OG T 840 DG T 841 CRYST1 98.731 98.731 202.271 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 0.010129 0.005848 0.000000 0.00000 SCALE2 0.000000 0.011695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004944 0.00000