HEADER TRANSFERASE/DNA 23-MAR-12 4EBD TITLE CONFORMATIONALLY RESTRAINED NORTH-METHANOCARBA-2'-DEOXYADENOSINE TITLE 2 CORRECTS THE ERROR-PRONE NATURE OF HUMAN DNA POLYMERASE IOTA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IOTA; COMPND 3 CHAIN: A; 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: 5'-D(P*AP*GP*GP*AP*CP*CP*(DOC))-3'; COMPND 10 CHAIN: P; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: 7-MER PRIMER DNA; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(P*CP*TP*GP*GP*GP*TP*CP*CP*T)-3'; COMPND 15 CHAIN: T; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: 9-MER TEMPLATE DNA 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBG101; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.L.EOFF,A.KETKAR,S.BANERJEE REVDAT 4 13-SEP-23 4EBD 1 REMARK LINK REVDAT 3 15-NOV-17 4EBD 1 REMARK REVDAT 2 11-JUL-12 4EBD 1 JRNL REVDAT 1 13-JUN-12 4EBD 0 JRNL AUTH A.KETKAR,M.K.ZAFAR,S.BANERJEE,V.E.MARQUEZ,M.EGLI,R.L.EOFF JRNL TITL A NUCLEOTIDE-ANALOGUE-INDUCED GAIN OF FUNCTION CORRECTS THE JRNL TITL 2 ERROR-PRONE NATURE OF HUMAN DNA POLYMERASE IOTA. JRNL REF J.AM.CHEM.SOC. V. 134 10698 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 22632140 JRNL DOI 10.1021/JA304176Q REMARK 2 REMARK 2 RESOLUTION. 2.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 18581 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1861 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 48.8968 - 6.0417 1.00 1469 164 0.2168 0.2422 REMARK 3 2 6.0417 - 4.7968 1.00 1355 151 0.2028 0.2515 REMARK 3 3 4.7968 - 4.1908 1.00 1338 148 0.1621 0.2185 REMARK 3 4 4.1908 - 3.8078 1.00 1312 145 0.1846 0.2168 REMARK 3 5 3.8078 - 3.5350 1.00 1300 145 0.2017 0.2717 REMARK 3 6 3.5350 - 3.3266 1.00 1308 145 0.2051 0.2975 REMARK 3 7 3.3266 - 3.1600 1.00 1275 141 0.2151 0.2942 REMARK 3 8 3.1600 - 3.0225 0.99 1281 145 0.2168 0.3105 REMARK 3 9 3.0225 - 2.9062 0.97 1250 142 0.2331 0.2899 REMARK 3 10 2.9062 - 2.8059 0.96 1227 136 0.2336 0.3247 REMARK 3 11 2.8059 - 2.7182 0.95 1217 134 0.2433 0.2866 REMARK 3 12 2.7182 - 2.6405 0.94 1202 134 0.2510 0.3287 REMARK 3 13 2.6405 - 2.5710 0.93 1186 131 0.2755 0.3325 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 42.13 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.830 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.720 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) : 7.18220 REMARK 3 B22 (A**2) : 7.18220 REMARK 3 B33 (A**2) : -8.63680 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 : 0.017 3441 REMARK 3 ANGLE : 1.370 4687 REMARK 3 CHIRALITY : 0.077 541 REMARK 3 PLANARITY : 0.008 538 REMARK 3 DIHEDRAL : 18.691 1349 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 26:99) REMARK 3 ORIGIN FOR THE GROUP (A): -1.7498 16.6301 21.2738 REMARK 3 T TENSOR REMARK 3 T11: 0.3865 T22: 0.2868 REMARK 3 T33: 0.3520 T12: -0.1487 REMARK 3 T13: 0.0683 T23: -0.0390 REMARK 3 L TENSOR REMARK 3 L11: 0.1037 L22: 0.2666 REMARK 3 L33: 0.6204 L12: -0.1634 REMARK 3 L13: -0.0741 L23: 0.0286 REMARK 3 S TENSOR REMARK 3 S11: -0.1015 S12: 0.1673 S13: 0.0029 REMARK 3 S21: 0.0677 S22: 0.0213 S23: 0.2821 REMARK 3 S31: 0.5600 S32: -0.1717 S33: -0.0151 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 100:286) REMARK 3 ORIGIN FOR THE GROUP (A): 11.2927 22.6029 2.9596 REMARK 3 T TENSOR REMARK 3 T11: 0.2197 T22: 0.1851 REMARK 3 T33: 0.1739 T12: -0.0012 REMARK 3 T13: -0.0347 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.6721 L22: 0.6048 REMARK 3 L33: 1.1654 L12: 0.6409 REMARK 3 L13: 0.2418 L23: 0.1179 REMARK 3 S TENSOR REMARK 3 S11: -0.0370 S12: -0.0331 S13: 0.0306 REMARK 3 S21: -0.1145 S22: -0.0313 S23: 0.0166 REMARK 3 S31: 0.0891 S32: 0.1379 S33: -0.0312 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 287:414) REMARK 3 ORIGIN FOR THE GROUP (A): 7.2556 41.0486 31.6550 REMARK 3 T TENSOR REMARK 3 T11: 0.5346 T22: 0.3730 REMARK 3 T33: 0.4097 T12: -0.2042 REMARK 3 T13: 0.1229 T23: -0.1275 REMARK 3 L TENSOR REMARK 3 L11: 0.6897 L22: 0.9812 REMARK 3 L33: 0.6669 L12: 0.3058 REMARK 3 L13: -0.0138 L23: -0.1956 REMARK 3 S TENSOR REMARK 3 S11: 0.2715 S12: -0.3375 S13: 0.2406 REMARK 3 S21: 0.3378 S22: -0.0860 S23: 0.2201 REMARK 3 S31: -0.5437 S32: 0.3833 S33: 0.0465 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'P' AND (RESSEQ 1:7) REMARK 3 ORIGIN FOR THE GROUP (A): 3.7487 40.9610 15.3276 REMARK 3 T TENSOR REMARK 3 T11: 0.5142 T22: 0.3311 REMARK 3 T33: 0.6058 T12: -0.1345 REMARK 3 T13: 0.0393 T23: -0.0728 REMARK 3 L TENSOR REMARK 3 L11: -0.0045 L22: 0.0032 REMARK 3 L33: 0.0411 L12: 0.0001 REMARK 3 L13: -0.0014 L23: 0.0133 REMARK 3 S TENSOR REMARK 3 S11: 0.0986 S12: 0.0118 S13: 0.0570 REMARK 3 S21: 0.1512 S22: -0.2748 S23: 0.2847 REMARK 3 S31: -0.3442 S32: 0.2839 S33: -0.0009 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'T' AND (RESSEQ 3:11) REMARK 3 ORIGIN FOR THE GROUP (A): 5.0689 36.2413 20.0059 REMARK 3 T TENSOR REMARK 3 T11: 0.4305 T22: 0.3827 REMARK 3 T33: 0.4127 T12: -0.1637 REMARK 3 T13: 0.0019 T23: -0.0431 REMARK 3 L TENSOR REMARK 3 L11: 0.0102 L22: 0.0573 REMARK 3 L33: 0.1786 L12: -0.0270 REMARK 3 L13: 0.0431 L23: -0.0649 REMARK 3 S TENSOR REMARK 3 S11: -0.1345 S12: -0.0992 S13: 0.3753 REMARK 3 S21: -0.1858 S22: -0.0293 S23: 0.3936 REMARK 3 S31: -0.4542 S32: -0.1138 S33: -0.0016 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 4EBD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071405. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.9 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) : 0.979 REMARK 200 MONOCHROMATOR : SI(220) SIDE BOUNCE 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 : 18978 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.570 REMARK 200 RESOLUTION RANGE LOW (A) : 84.676 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 51.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.40900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3GV5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM TRIS-HCL, PH 7.9, 5% GLYCEROL, REMARK 280 10 MM 2-MERCAPTOETHANOL, 150 MM CALCIUM CHLORIDE, 12% PEG3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 135.15933 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 67.57967 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 101.36950 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 33.78983 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 168.94917 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 135.15933 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 67.57967 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 33.78983 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 101.36950 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 168.94917 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: 4960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, T REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 677 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 LEU A 3 REMARK 465 ALA A 4 REMARK 465 ASP A 5 REMARK 465 VAL A 6 REMARK 465 GLY A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLN A 13 REMARK 465 GLY A 14 REMARK 465 VAL A 15 REMARK 465 HIS A 16 REMARK 465 ASP A 17 REMARK 465 GLN A 18 REMARK 465 VAL A 19 REMARK 465 LEU A 20 REMARK 465 PRO A 21 REMARK 465 THR A 22 REMARK 465 PRO A 23 REMARK 465 ASN A 24 REMARK 465 ALA A 25 REMARK 465 GLY A 336 REMARK 465 SER A 350 REMARK 465 SER A 351 REMARK 465 GLU A 352 REMARK 465 LYS A 353 REMARK 465 HIS A 354 REMARK 465 TYR A 355 REMARK 465 LEU A 372 REMARK 465 GLY A 373 REMARK 465 THR A 374 REMARK 465 GLY A 375 REMARK 465 ASN A 376 REMARK 465 TYR A 377 REMARK 465 ALA A 415 REMARK 465 LEU A 416 REMARK 465 ASN A 417 REMARK 465 THR A 418 REMARK 465 ALA A 419 REMARK 465 LYS A 420 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 310 CE 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 OP2 DG T 6 O1 GOL A 505 2.15 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 P 2 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DG P 2 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA P 4 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC P 5 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 DC T 3 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG T 5 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 DT T 11 O4' - C4' - C3' ANGL. DEV. = -5.6 DEGREES REMARK 500 DT T 11 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES REMARK 500 DT T 11 C3' - C2' - C1' ANGL. DEV. = -8.6 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 A 37 63.34 24.91 REMARK 500 ASP A 52 -22.15 75.95 REMARK 500 LYS A 60 -123.10 49.79 REMARK 500 GLU A 69 -2.33 -52.76 REMARK 500 GLU A 86 14.21 -69.89 REMARK 500 LYS A 87 -11.04 -141.54 REMARK 500 CYS A 88 90.20 -170.69 REMARK 500 CYS A 311 99.12 -162.16 REMARK 500 CYS A 333 -120.19 -67.17 REMARK 500 GLN A 334 -128.33 52.57 REMARK 500 ILE A 369 36.40 -77.20 REMARK 500 VAL A 379 -18.94 -152.35 REMARK 500 CYS A 411 -157.00 -127.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 259 0.09 SIDE CHAIN 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 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 34 OD2 REMARK 620 2 GLU A 127 OE2 90.2 REMARK 620 3 HOH A 651 O 168.9 100.3 REMARK 620 4 HOH A 662 O 83.1 161.3 88.0 REMARK 620 5 HOH A 707 O 59.3 112.9 112.5 78.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 34 OD1 REMARK 620 2 LEU A 35 O 93.3 REMARK 620 3 0OJ A 501 OAF 111.0 77.0 REMARK 620 4 0OJ A 501 OAI 169.5 79.8 75.2 REMARK 620 5 0OJ A 501 OAC 110.1 150.4 109.4 74.4 REMARK 620 6 0OJ A 501 OAT 140.2 122.0 65.4 49.7 46.4 REMARK 620 7 HOH A 722 O 62.0 72.1 49.9 122.1 134.7 108.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 504 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 237 O REMARK 620 2 ILE A 239 O 87.1 REMARK 620 3 ILE A 242 O 77.4 69.2 REMARK 620 4 HOH A 702 O 100.2 112.1 177.3 REMARK 620 5 HOH A 708 O 71.7 140.3 133.5 44.0 REMARK 620 6 DC P 6 OP1 156.4 83.9 79.0 103.4 127.2 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 0OJ A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T3N RELATED DB: PDB REMARK 900 RELATED ID: 2ALZ RELATED DB: PDB REMARK 900 RELATED ID: 3GV5 RELATED DB: PDB REMARK 900 RELATED ID: 3GV7 RELATED DB: PDB REMARK 900 RELATED ID: 3GV8 RELATED DB: PDB REMARK 900 RELATED ID: 3H40 RELATED DB: PDB REMARK 900 RELATED ID: 4EBC RELATED DB: PDB REMARK 900 RELATED ID: 4EBE RELATED DB: PDB DBREF 4EBD A 1 420 UNP Q9UNA4 POLI_HUMAN 26 445 DBREF 4EBD P 1 7 PDB 4EBD 4EBD 1 7 DBREF 4EBD T 3 11 PDB 4EBD 4EBD 3 11 SEQRES 1 A 420 MET GLU LEU ALA ASP VAL GLY ALA ALA ALA SER SER GLN SEQRES 2 A 420 GLY VAL HIS ASP GLN VAL LEU PRO THR PRO ASN ALA SER SEQRES 3 A 420 SER ARG VAL ILE VAL HIS VAL ASP LEU ASP CYS PHE TYR SEQRES 4 A 420 ALA GLN VAL GLU MET ILE SER ASN PRO GLU LEU LYS ASP SEQRES 5 A 420 LYS PRO LEU GLY VAL GLN GLN LYS TYR LEU VAL VAL THR SEQRES 6 A 420 CYS ASN TYR GLU ALA ARG LYS LEU GLY VAL LYS LYS LEU SEQRES 7 A 420 MET ASN VAL ARG ASP ALA LYS GLU LYS CYS PRO GLN LEU SEQRES 8 A 420 VAL LEU VAL ASN GLY GLU ASP LEU THR ARG TYR ARG GLU SEQRES 9 A 420 MET SER TYR LYS VAL THR GLU LEU LEU GLU GLU PHE SER SEQRES 10 A 420 PRO VAL VAL GLU ARG LEU GLY PHE ASP GLU ASN PHE VAL SEQRES 11 A 420 ASP LEU THR GLU MET VAL GLU LYS ARG LEU GLN GLN LEU SEQRES 12 A 420 GLN SER ASP GLU LEU SER ALA VAL THR VAL SER GLY HIS SEQRES 13 A 420 VAL TYR ASN ASN GLN SER ILE ASN LEU LEU ASP VAL LEU SEQRES 14 A 420 HIS ILE ARG LEU LEU VAL GLY SER GLN ILE ALA ALA GLU SEQRES 15 A 420 MET ARG GLU ALA MET TYR ASN GLN LEU GLY LEU THR GLY SEQRES 16 A 420 CYS ALA GLY VAL ALA SER ASN LYS LEU LEU ALA LYS LEU SEQRES 17 A 420 VAL SER GLY VAL PHE LYS PRO ASN GLN GLN THR VAL LEU SEQRES 18 A 420 LEU PRO GLU SER CYS GLN HIS LEU ILE HIS SER LEU ASN SEQRES 19 A 420 HIS ILE LYS GLU ILE PRO GLY ILE GLY TYR LYS THR ALA SEQRES 20 A 420 LYS CYS LEU GLU ALA LEU GLY ILE ASN SER VAL ARG ASP SEQRES 21 A 420 LEU GLN THR PHE SER PRO LYS ILE LEU GLU LYS GLU LEU SEQRES 22 A 420 GLY ILE SER VAL ALA GLN ARG ILE GLN LYS LEU SER PHE SEQRES 23 A 420 GLY GLU ASP ASN SER PRO VAL ILE LEU SER GLY PRO PRO SEQRES 24 A 420 GLN SER PHE SER GLU GLU ASP SER PHE LYS LYS CYS SER SEQRES 25 A 420 SER GLU VAL GLU ALA LYS ASN LYS ILE GLU GLU LEU LEU SEQRES 26 A 420 ALA SER LEU LEU ASN ARG VAL CYS GLN ASP GLY ARG LYS SEQRES 27 A 420 PRO HIS THR VAL ARG LEU ILE ILE ARG ARG TYR SER SER SEQRES 28 A 420 GLU LYS HIS TYR GLY ARG GLU SER ARG GLN CYS PRO ILE SEQRES 29 A 420 PRO SER HIS VAL ILE GLN LYS LEU GLY THR GLY ASN TYR SEQRES 30 A 420 ASP VAL MET THR PRO MET VAL ASP ILE LEU MET LYS LEU SEQRES 31 A 420 PHE ARG ASN MET VAL ASN VAL LYS MET PRO PHE HIS LEU SEQRES 32 A 420 THR LEU LEU SER VAL CYS PHE CYS ASN LEU LYS ALA LEU SEQRES 33 A 420 ASN THR ALA LYS SEQRES 1 P 7 DA DG DG DA DC DC DOC SEQRES 1 T 9 DC DT DG DG DG DT DC DC DT MODRES 4EBD DOC P 7 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC P 7 30 HET 0OJ A 501 45 HET CA A 502 1 HET CA A 503 1 HET CA A 504 1 HET GOL A 505 6 HET GOL A 506 6 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM 0OJ SOUTH-METHANOCARBA-2'-DEOXYADENOSINE TRIPHOSPHATE HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 0OJ C12 H18 N5 O11 P3 FORMUL 5 CA 3(CA 2+) FORMUL 8 GOL 2(C3 H8 O3) FORMUL 10 HOH *146(H2 O) HELIX 1 1 CYS A 37 ASN A 47 1 11 HELIX 2 2 ASN A 67 LYS A 72 1 6 HELIX 3 3 VAL A 81 GLU A 86 1 6 HELIX 4 4 LEU A 99 SER A 117 1 19 HELIX 5 5 LEU A 132 LEU A 143 1 12 HELIX 6 6 ASP A 146 ALA A 150 5 5 HELIX 7 7 ASN A 159 GLN A 161 5 3 HELIX 8 8 ASP A 167 GLY A 192 1 26 HELIX 9 9 ASN A 202 SER A 210 1 9 HELIX 10 10 LEU A 222 GLU A 224 5 3 HELIX 11 11 SER A 225 SER A 232 1 8 HELIX 12 12 HIS A 235 ILE A 239 5 5 HELIX 13 13 GLY A 243 GLU A 251 1 9 HELIX 14 14 ALA A 252 GLY A 254 5 3 HELIX 15 15 SER A 257 PHE A 264 1 8 HELIX 16 16 SER A 265 GLY A 274 1 10 HELIX 17 17 GLY A 274 SER A 285 1 12 HELIX 18 18 SER A 313 VAL A 332 1 20 HELIX 19 19 PRO A 365 GLN A 370 5 6 HELIX 20 20 VAL A 379 VAL A 395 1 17 SHEET 1 A 6 VAL A 120 LEU A 123 0 SHEET 2 A 6 GLU A 127 ASP A 131 -1 O PHE A 129 N GLU A 121 SHEET 3 A 6 ILE A 30 LEU A 35 -1 N VAL A 33 O ASN A 128 SHEET 4 A 6 GLY A 195 ALA A 200 -1 O CYS A 196 N ASP A 34 SHEET 5 A 6 GLN A 218 VAL A 220 1 O THR A 219 N ALA A 197 SHEET 6 A 6 HIS A 156 VAL A 157 1 N HIS A 156 O GLN A 218 SHEET 1 B 4 MET A 79 ASN A 80 0 SHEET 2 B 4 LEU A 62 CYS A 66 -1 N VAL A 63 O MET A 79 SHEET 3 B 4 LEU A 55 GLN A 59 -1 N GLN A 59 O LEU A 62 SHEET 4 B 4 VAL A 92 ASN A 95 1 O VAL A 94 N GLN A 58 SHEET 1 C 4 PHE A 302 SER A 307 0 SHEET 2 C 4 LEU A 405 LEU A 413 -1 O LEU A 406 N ASP A 306 SHEET 3 C 4 PRO A 339 ARG A 347 -1 N ARG A 343 O CYS A 409 SHEET 4 C 4 ARG A 357 PRO A 363 -1 O CYS A 362 N VAL A 342 LINK O3' DC P 6 P DOC P 7 1555 1555 1.60 LINK OD2 ASP A 34 CA CA A 502 1555 1555 2.88 LINK OD1 ASP A 34 CA CA A 503 1555 1555 2.75 LINK O LEU A 35 CA CA A 503 1555 1555 2.77 LINK OE2 GLU A 127 CA CA A 502 1555 1555 2.90 LINK O LYS A 237 CA CA A 504 1555 1555 2.91 LINK O ILE A 239 CA CA A 504 1555 1555 3.19 LINK O ILE A 242 CA CA A 504 1555 1555 2.99 LINK OAF 0OJ A 501 CA CA A 503 1555 1555 2.71 LINK OAI 0OJ A 501 CA CA A 503 1555 1555 2.85 LINK OAC 0OJ A 501 CA CA A 503 1555 1555 3.12 LINK OAT 0OJ A 501 CA CA A 503 1555 1555 3.18 LINK CA CA A 502 O HOH A 651 1555 1555 2.99 LINK CA CA A 502 O HOH A 662 1555 1555 3.01 LINK CA CA A 502 O HOH A 707 1555 1555 3.03 LINK CA CA A 503 O HOH A 722 1555 1555 3.15 LINK CA CA A 504 O HOH A 702 1555 1555 3.06 LINK CA CA A 504 O HOH A 708 1555 1555 3.01 LINK CA CA A 504 OP1 DC P 6 1555 1555 2.90 CISPEP 1 LYS A 214 PRO A 215 0 -9.25 SITE 1 AC1 24 LEU A 35 CYS A 37 PHE A 38 TYR A 39 SITE 2 AC1 24 VAL A 64 THR A 65 TYR A 68 ARG A 71 SITE 3 AC1 24 LYS A 77 LEU A 78 ASP A 126 LYS A 214 SITE 4 AC1 24 CA A 503 HOH A 616 HOH A 650 HOH A 651 SITE 5 AC1 24 HOH A 652 HOH A 662 HOH A 722 DOC P 7 SITE 6 AC1 24 HOH P 101 DT T 4 DG T 5 HOH T 110 SITE 1 AC2 5 ASP A 34 GLU A 127 HOH A 651 HOH A 662 SITE 2 AC2 5 HOH A 707 SITE 1 AC3 4 ASP A 34 LEU A 35 ASP A 126 0OJ A 501 SITE 1 AC4 6 LYS A 237 ILE A 239 ILE A 242 HOH A 702 SITE 2 AC4 6 HOH A 708 DC P 6 SITE 1 AC5 8 ASP A 98 GLU A 304 GLU A 305 HOH A 611 SITE 2 AC5 8 HOH A 629 HOH A 701 DG T 6 HOH T 103 SITE 1 AC6 7 GLU A 305 ARG A 357 HOH A 657 HOH A 658 SITE 2 AC6 7 DG T 5 DG T 6 DG T 7 CRYST1 97.776 97.776 202.739 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 0.010227 0.005905 0.000000 0.00000 SCALE2 0.000000 0.011810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004932 0.00000