HEADER TRANSFERASE/DNA 01-MAY-12 4EYI TITLE HUMAN DNA POLYMERASE IOTA INCORPORATING DATP OPPOSITE N- TITLE 2 (DEOXYGUANOSIN-8-YL)-1-AMINOPYRENE LESION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IOTA; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: UNP RESIDUES 26-445; 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 TEMPLATE; COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA PRIMER; 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 OTHER_DETAILS: SYNTHESIZED; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHESIZED KEYWDS DNA POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.KIROUAC,H.LING REVDAT 3 28-FEB-24 4EYI 1 REMARK LINK REVDAT 2 20-FEB-13 4EYI 1 JRNL REVDAT 1 09-JAN-13 4EYI 0 JRNL AUTH K.N.KIROUAC,A.K.BASU,H.LING JRNL TITL REPLICATION OF A CARCINOGENIC NITROPYRENE DNA LESION BY JRNL TITL 2 HUMAN Y-FAMILY DNA POLYMERASE. JRNL REF NUCLEIC ACIDS RES. V. 41 2060 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23268450 JRNL DOI 10.1093/NAR/GKS1296 REMARK 2 REMARK 2 RESOLUTION. 2.90 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 12929 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1028 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 32.3583 - 5.5401 0.97 1806 159 0.2077 0.2406 REMARK 3 2 5.5401 - 4.4008 0.98 1711 151 0.1951 0.2242 REMARK 3 3 4.4008 - 3.8456 0.99 1703 136 0.1918 0.2414 REMARK 3 4 3.8456 - 3.4944 0.99 1676 153 0.2266 0.3144 REMARK 3 5 3.4944 - 3.2442 1.00 1690 141 0.2433 0.3045 REMARK 3 6 3.2442 - 3.0531 1.00 1656 147 0.2716 0.3516 REMARK 3 7 3.0531 - 2.9003 0.99 1659 141 0.3369 0.3646 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.31 REMARK 3 B_SOL : 54.68 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.600 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) : -1.88470 REMARK 3 B22 (A**2) : -1.88470 REMARK 3 B33 (A**2) : 3.76950 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 3393 REMARK 3 ANGLE : 1.140 4657 REMARK 3 CHIRALITY : 0.070 541 REMARK 3 PLANARITY : 0.004 536 REMARK 3 DIHEDRAL : 19.982 1304 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 27:105) REMARK 3 ORIGIN FOR THE GROUP (A): -0.3788 16.9667 22.2549 REMARK 3 T TENSOR REMARK 3 T11: 0.5160 T22: 0.6304 REMARK 3 T33: 0.5091 T12: -0.1835 REMARK 3 T13: 0.0478 T23: -0.1154 REMARK 3 L TENSOR REMARK 3 L11: 0.6764 L22: 1.7465 REMARK 3 L33: 0.9783 L12: 0.0226 REMARK 3 L13: -0.1447 L23: 0.6946 REMARK 3 S TENSOR REMARK 3 S11: -0.1959 S12: -0.0787 S13: 0.0164 REMARK 3 S21: 0.3358 S22: -0.3093 S23: 0.1954 REMARK 3 S31: 0.5020 S32: -0.4836 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESID 106:152) REMARK 3 ORIGIN FOR THE GROUP (A): 21.5455 22.2390 7.2744 REMARK 3 T TENSOR REMARK 3 T11: 0.5016 T22: 0.4876 REMARK 3 T33: 0.5972 T12: -0.0306 REMARK 3 T13: -0.0630 T23: 0.1513 REMARK 3 L TENSOR REMARK 3 L11: 0.9044 L22: 0.5164 REMARK 3 L33: 0.8347 L12: 0.3656 REMARK 3 L13: 1.0494 L23: -0.0979 REMARK 3 S TENSOR REMARK 3 S11: -0.0788 S12: -0.0313 S13: 0.4298 REMARK 3 S21: 0.0097 S22: -0.0927 S23: -0.3748 REMARK 3 S31: 0.2255 S32: 0.2027 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN B AND RESID 153:194) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1508 15.0833 1.2059 REMARK 3 T TENSOR REMARK 3 T11: 0.5345 T22: 0.4898 REMARK 3 T33: 0.5325 T12: 0.0467 REMARK 3 T13: -0.0450 T23: 0.0672 REMARK 3 L TENSOR REMARK 3 L11: 0.1341 L22: 0.3472 REMARK 3 L33: 0.2355 L12: -0.1024 REMARK 3 L13: 0.0680 L23: 0.5236 REMARK 3 S TENSOR REMARK 3 S11: 0.0357 S12: 0.1005 S13: -0.0969 REMARK 3 S21: -0.0480 S22: -0.2683 S23: -0.2215 REMARK 3 S31: 0.1869 S32: -0.0346 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 195:301) REMARK 3 ORIGIN FOR THE GROUP (A): 2.7546 32.5213 0.0988 REMARK 3 T TENSOR REMARK 3 T11: 0.5252 T22: 0.4929 REMARK 3 T33: 0.5525 T12: 0.0150 REMARK 3 T13: -0.1555 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 0.5916 L22: 0.9132 REMARK 3 L33: 0.9993 L12: 0.0596 REMARK 3 L13: 1.1706 L23: 0.0914 REMARK 3 S TENSOR REMARK 3 S11: -0.0641 S12: -0.0840 S13: 0.0669 REMARK 3 S21: -0.1583 S22: -0.1424 S23: 0.0657 REMARK 3 S31: -0.0581 S32: 0.0084 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 302:416) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9041 44.2383 33.8333 REMARK 3 T TENSOR REMARK 3 T11: 0.8700 T22: 1.1774 REMARK 3 T33: 0.7622 T12: -0.3058 REMARK 3 T13: 0.0232 T23: -0.0519 REMARK 3 L TENSOR REMARK 3 L11: 0.3751 L22: 1.7605 REMARK 3 L33: 2.3736 L12: -0.1511 REMARK 3 L13: 0.4729 L23: 0.9019 REMARK 3 S TENSOR REMARK 3 S11: 0.7461 S12: -0.2865 S13: -0.1149 REMARK 3 S21: 0.5167 S22: -0.3243 S23: -0.1358 REMARK 3 S31: 0.3866 S32: -0.5639 S33: -0.0000 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 4EYI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072228. 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 : NULL 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 : 12929 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 32.356 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <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 (%): 53.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 5000MME, 0.2 M 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 129.46867 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 64.73433 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 97.10150 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 32.36717 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 161.83583 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 129.46867 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 64.73433 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 32.36717 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 97.10150 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 161.83583 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: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 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 350 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 356 REMARK 465 LEU B 372 REMARK 465 GLY B 373 REMARK 465 THR B 374 REMARK 465 GLY B 375 REMARK 465 ASN B 376 REMARK 465 TYR B 377 REMARK 465 ASN B 417 REMARK 465 THR B 418 REMARK 465 ALA B 419 REMARK 465 LYS B 420 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 B 51 CG CD CE NZ 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 GLU B 147 CG CD OE1 OE2 REMARK 470 LYS B 310 CG CD CE NZ REMARK 470 ASN B 319 CG OD1 ND2 REMARK 470 CYS B 333 SG REMARK 470 LYS B 338 CG CD CE NZ REMARK 470 GLN B 370 CG CD OE1 NE2 REMARK 470 LYS B 371 CD CE NZ REMARK 470 ASP B 385 CG OD1 OD2 REMARK 470 LEU B 416 CG CD1 CD2 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 O GLU B 316 CD LYS B 320 2.02 REMARK 500 O SER B 313 CZ PHE B 401 2.13 REMARK 500 O ALA B 186 O ASN B 189 2.18 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 GLU B 316 CB - CA - C ANGL. DEV. = -21.7 DEGREES REMARK 500 ALA B 317 N - CA - C ANGL. DEV. = -16.2 DEGREES REMARK 500 LEU B 403 CB - CA - C ANGL. DEV. = -14.7 DEGREES REMARK 500 LEU B 403 N - CA - C ANGL. DEV. = 18.5 DEGREES REMARK 500 DG8 T 840 C3' - O3' - P ANGL. DEV. = 10.0 DEGREES REMARK 500 DG T 841 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DG T 841 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA P 867 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG P 868 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA P 870 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC P 871 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DC P 873 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DC P 873 O4' - C1' - N1 ANGL. DEV. = 2.8 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 59.21 32.82 REMARK 500 LYS B 60 -139.45 57.52 REMARK 500 GLN B 142 4.00 -65.00 REMARK 500 GLU B 147 21.12 -76.76 REMARK 500 VAL B 151 -57.64 65.71 REMARK 500 THR B 152 173.98 69.11 REMARK 500 LEU B 165 -8.10 -59.57 REMARK 500 GLN B 190 -26.70 87.57 REMARK 500 GLU B 224 2.90 -68.54 REMARK 500 SER B 312 12.63 -143.38 REMARK 500 SER B 313 -153.91 -112.83 REMARK 500 GLU B 316 -14.80 72.77 REMARK 500 ARG B 348 -168.11 -104.65 REMARK 500 PRO B 365 158.06 -44.56 REMARK 500 ILE B 369 80.17 -63.35 REMARK 500 GLN B 370 36.12 -152.63 REMARK 500 MET B 380 -74.72 -75.14 REMARK 500 LYS B 398 37.06 -81.27 REMARK 500 PHE B 401 -58.85 -139.85 REMARK 500 HIS B 402 129.48 45.15 REMARK 500 THR B 404 -4.57 85.17 REMARK 500 CYS B 411 -164.41 -128.57 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 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 34 OD1 REMARK 620 2 LEU B 35 O 80.9 REMARK 620 3 ASP B 126 OD1 81.0 79.9 REMARK 620 4 DTP B 501 O1G 109.7 112.1 164.7 REMARK 620 5 DTP B 501 O1B 157.8 88.0 78.2 92.2 REMARK 620 6 DTP B 501 O3A 140.9 138.0 105.5 59.2 54.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 126 OD1 REMARK 620 2 GLU B 127 OE2 136.1 REMARK 620 3 DTP B 501 O1A 95.2 128.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 237 O REMARK 620 2 ILE B 242 O 75.2 REMARK 620 3 HOH B 602 O 107.5 144.2 REMARK 620 4 DC P 872 OP1 143.7 74.8 85.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTP B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EYH RELATED DB: PDB DBREF 4EYI B 1 420 UNP Q9UNA4 POLI_HUMAN 26 445 DBREF 4EYI T 840 847 PDB 4EYI 4EYI 840 847 DBREF 4EYI P 867 873 PDB 4EYI 4EYI 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 8 DG8 DG DG DG DT DC DC DT SEQRES 1 P 7 DA DG DG DA DC DC DC MODRES 4EYI DG8 T 840 DG HET DG8 T 840 39 HET DTP B 501 30 HET MG B 502 1 HET MG B 503 1 HET MG B 504 1 HETNAM DG8 2'-DEOXY-8-(PYREN-1-YLAMINO)GUANOSINE 5'-(DIHYDROGEN HETNAM 2 DG8 PHOSPHATE) HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 DG8 C26 H23 N6 O7 P FORMUL 4 DTP C10 H16 N5 O12 P3 FORMUL 5 MG 3(MG 2+) FORMUL 8 HOH *28(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 TYR B 68 ARG B 71 5 4 HELIX 4 4 VAL B 81 CYS B 88 1 8 HELIX 5 5 LEU B 99 GLU B 115 1 17 HELIX 6 6 LEU B 132 GLN B 142 1 11 HELIX 7 7 GLN B 144 LEU B 148 5 5 HELIX 8 8 ASN B 159 GLN B 161 5 3 HELIX 9 9 ASP B 167 GLY B 192 1 26 HELIX 10 10 ASN B 202 SER B 210 1 9 HELIX 11 11 LEU B 222 GLU B 224 5 3 HELIX 12 12 SER B 225 SER B 232 1 8 HELIX 13 13 HIS B 235 ILE B 239 5 5 HELIX 14 14 GLY B 243 ALA B 252 1 10 HELIX 15 15 SER B 257 PHE B 264 1 8 HELIX 16 16 SER B 265 GLY B 274 1 10 HELIX 17 17 GLY B 274 SER B 285 1 12 HELIX 18 18 ALA B 317 GLY B 336 1 20 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 CYS B 196 N ASP B 34 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 SER B 307 0 SHEET 2 C 4 LEU B 405 LYS B 414 -1 O LEU B 406 N ASP B 306 SHEET 3 C 4 LYS B 338 ILE B 346 -1 N HIS B 340 O ASN B 412 SHEET 4 C 4 GLU B 358 PRO B 363 -1 O ARG B 360 N LEU B 344 LINK OD1 ASP B 34 MG MG B 503 1555 1555 2.45 LINK O LEU B 35 MG MG B 503 1555 1555 2.66 LINK OD1 ASP B 126 MG MG B 502 1555 1555 2.92 LINK OD1 ASP B 126 MG MG B 503 1555 1555 2.65 LINK OE2 GLU B 127 MG MG B 502 1555 1555 2.71 LINK O LYS B 237 MG MG B 504 1555 1555 2.65 LINK O ILE B 242 MG MG B 504 1555 1555 2.93 LINK O1A DTP B 501 MG MG B 502 1555 1555 2.44 LINK O1G DTP B 501 MG MG B 503 1555 1555 2.41 LINK O1B DTP B 501 MG MG B 503 1555 1555 2.72 LINK O3A DTP B 501 MG MG B 503 1555 1555 2.92 LINK MG MG B 504 O HOH B 602 1555 1555 2.87 LINK MG MG B 504 OP1 DC P 872 1555 1555 2.72 CISPEP 1 SER B 149 ALA B 150 0 -1.76 CISPEP 2 LYS B 214 PRO B 215 0 -5.04 CISPEP 3 LYS B 414 ALA B 415 0 6.26 SITE 1 AC1 14 CYS B 37 PHE B 38 TYR B 39 VAL B 64 SITE 2 AC1 14 THR B 65 TYR B 68 ARG B 71 LYS B 77 SITE 3 AC1 14 ASP B 126 LYS B 214 MG B 502 MG B 503 SITE 4 AC1 14 DC P 873 DG8 T 840 SITE 1 AC2 6 ASP B 34 ASP B 126 GLU B 127 DTP B 501 SITE 2 AC2 6 MG B 503 DC P 873 SITE 1 AC3 5 ASP B 34 LEU B 35 ASP B 126 DTP B 501 SITE 2 AC3 5 MG B 502 SITE 1 AC4 5 LYS B 237 ILE B 239 ILE B 242 HOH B 602 SITE 2 AC4 5 DC P 872 CRYST1 98.850 98.850 194.203 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 0.010116 0.005841 0.000000 0.00000 SCALE2 0.000000 0.011681 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005149 0.00000