HEADER TRANSFERASE/DNA 11-APR-12 4ELT TITLE SNAPSHOT OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS TITLE 2 AQUATICUS PROCESSING MODIFIED PYRIMIDINES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TAQ POLYMERASE 1; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: DNA PRIMER; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- COMPND 14 3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: DNA TEMPLATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POLA, POL1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC DNA; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC DNA; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, MODIFIED NUCLEOTIDES, A FAMILY, DNA SYNTHESIS, RIGID KEYWDS 2 LINKER, NON-NATURAL NUCLEOTIDE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MARX,K.DIEDERICHS,S.OBEID REVDAT 2 13-SEP-23 4ELT 1 REMARK LINK REVDAT 1 27-MAR-13 4ELT 0 JRNL AUTH S.OBEID,H.BUSSKAMP,W.WELTE,K.DIEDERICHS,A.MARX JRNL TITL INTERACTIONS OF NON-POLAR AND "CLICK-ABLE" NUCLEOTIDES IN JRNL TITL 2 THE CONFINES OF A DNA POLYMERASE ACTIVE SITE. JRNL REF CHEM.COMMUN.(CAMB.) V. 48 8320 2012 JRNL REFN ISSN 1359-7345 JRNL PMID 22766607 JRNL DOI 10.1039/C2CC34181F REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 31776 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1598 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 47.1486 - 4.8911 1.00 2893 163 0.1609 0.1893 REMARK 3 2 4.8911 - 3.8828 1.00 2802 152 0.1347 0.1736 REMARK 3 3 3.8828 - 3.3922 1.00 2745 162 0.1452 0.1860 REMARK 3 4 3.3922 - 3.0821 1.00 2761 148 0.1539 0.2033 REMARK 3 5 3.0821 - 2.8612 1.00 2757 142 0.1566 0.2220 REMARK 3 6 2.8612 - 2.6925 1.00 2748 151 0.1670 0.2223 REMARK 3 7 2.6925 - 2.5577 1.00 2740 148 0.1656 0.2589 REMARK 3 8 2.5577 - 2.4464 1.00 2721 151 0.1900 0.2725 REMARK 3 9 2.4464 - 2.3522 1.00 2750 123 0.1965 0.2712 REMARK 3 10 2.3522 - 2.2710 1.00 2723 139 0.2029 0.2727 REMARK 3 11 2.2710 - 2.2000 0.92 2538 119 0.2399 0.2984 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 : 0.37 REMARK 3 B_SOL : 39.37 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.020 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) : 7.60720 REMARK 3 B22 (A**2) : 7.60720 REMARK 3 B33 (A**2) : 3.85070 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 : 0.007 5135 REMARK 3 ANGLE : 1.129 7056 REMARK 3 CHIRALITY : 0.070 767 REMARK 3 PLANARITY : 0.005 816 REMARK 3 DIHEDRAL : 16.647 1990 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 294:452) REMARK 3 ORIGIN FOR THE GROUP (A): 39.0974 -41.1404 -18.5373 REMARK 3 T TENSOR REMARK 3 T11: 0.3305 T22: 0.2089 REMARK 3 T33: 0.3442 T12: -0.0432 REMARK 3 T13: 0.1020 T23: -0.0369 REMARK 3 L TENSOR REMARK 3 L11: 0.5706 L22: 2.7393 REMARK 3 L33: 1.7269 L12: -0.2335 REMARK 3 L13: -0.1565 L23: -0.1224 REMARK 3 S TENSOR REMARK 3 S11: -0.0934 S12: 0.0796 S13: -0.3090 REMARK 3 S21: -0.4571 S22: -0.0192 S23: -0.4644 REMARK 3 S31: 0.3708 S32: 0.1280 S33: 0.0910 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 453:603) REMARK 3 ORIGIN FOR THE GROUP (A): 36.1531 -11.0711 1.4402 REMARK 3 T TENSOR REMARK 3 T11: 0.1913 T22: 0.1402 REMARK 3 T33: 0.1889 T12: -0.0100 REMARK 3 T13: 0.0099 T23: 0.0088 REMARK 3 L TENSOR REMARK 3 L11: 1.3109 L22: 1.2708 REMARK 3 L33: 1.8219 L12: 0.7712 REMARK 3 L13: 0.2856 L23: 0.6166 REMARK 3 S TENSOR REMARK 3 S11: 0.0067 S12: -0.1316 S13: 0.0992 REMARK 3 S21: -0.0141 S22: -0.0318 S23: 0.0802 REMARK 3 S31: -0.2960 S32: 0.0235 S33: 0.0232 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 604:685) REMARK 3 ORIGIN FOR THE GROUP (A): 11.5243 -13.3665 -8.4566 REMARK 3 T TENSOR REMARK 3 T11: 0.3585 T22: 0.3959 REMARK 3 T33: 0.2777 T12: 0.1116 REMARK 3 T13: -0.0333 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 1.5630 L22: 0.6235 REMARK 3 L33: 2.4637 L12: 0.6092 REMARK 3 L13: -0.6030 L23: -0.1462 REMARK 3 S TENSOR REMARK 3 S11: -0.0079 S12: -0.1489 S13: 0.4405 REMARK 3 S21: -0.0291 S22: 0.0109 S23: 0.2710 REMARK 3 S31: -0.6715 S32: -0.6073 S33: -0.0346 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 686:832) REMARK 3 ORIGIN FOR THE GROUP (A): 17.3218 -24.6346 -13.1420 REMARK 3 T TENSOR REMARK 3 T11: 0.1880 T22: 0.2687 REMARK 3 T33: 0.1808 T12: -0.0003 REMARK 3 T13: -0.0206 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 1.5049 L22: 1.0728 REMARK 3 L33: 2.0908 L12: 0.5879 REMARK 3 L13: -0.3128 L23: -0.2790 REMARK 3 S TENSOR REMARK 3 S11: -0.0919 S12: 0.1020 S13: -0.0170 REMARK 3 S21: -0.1239 S22: 0.1035 S23: 0.1298 REMARK 3 S31: -0.0895 S32: -0.5012 S33: -0.0156 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 4ELT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071779. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR WITH DUAL REMARK 200 CHANNEL CUT CRYSTALS (DCCM) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32014 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 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 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.80200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.060 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.7.2_869 REMARK 200 STARTING MODEL: 3OJS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA CACODYLATE PH=6.5, 0.2 M REMARK 280 NH4(OAC), 10 MM MG(OAC)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 30.33467 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 60.66933 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.66933 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 30.33467 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: 9600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 A1147 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 ALA A 293 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 346 CG CD CE NZ 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 O HOH A 1162 O HOH A 1162 6554 2.19 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 B 108 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC B 111 C3' - O3' - P ANGL. DEV. = -11.0 DEGREES REMARK 500 DA C 201 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA C 202 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG C 205 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 207 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT C 212 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG C 214 C1' - O4' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC C 216 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 ASP A 381 104.78 -166.71 REMARK 500 THR A 399 -164.72 -105.76 REMARK 500 VAL A 433 -70.59 -120.59 REMARK 500 TYR A 545 -53.92 -126.55 REMARK 500 VAL A 586 -17.35 -159.75 REMARK 500 ALA A 653 42.86 -103.89 REMARK 500 HIS A 784 -66.72 74.52 REMARK 500 TYR A 811 99.73 -169.88 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 A 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 85.7 REMARK 620 3 ASP A 785 OD2 87.0 87.4 REMARK 620 4 0R5 A 901 O2G 91.9 99.1 173.3 REMARK 620 5 0R5 A 901 O2B 176.2 96.5 89.9 90.9 REMARK 620 6 0R5 A 901 O1A 92.0 171.8 84.7 88.8 85.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 903 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 ASP A 785 OD1 108.0 REMARK 620 3 0R5 A 901 O1A 104.5 86.0 REMARK 620 4 HOH A1001 O 97.1 94.0 157.3 REMARK 620 5 HOH A1002 O 94.2 156.8 82.1 89.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 432 O REMARK 620 2 HOH C 433 O 111.0 REMARK 620 3 HOH C 434 O 119.4 95.0 REMARK 620 4 HOH C 435 O 106.5 106.6 117.2 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 0R5 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 909 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 910 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 911 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 912 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 913 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 914 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OJS RELATED DB: PDB REMARK 900 RELATED ID: 3OJU RELATED DB: PDB REMARK 900 RELATED ID: 4ELU RELATED DB: PDB REMARK 900 RELATED ID: 4ELV RELATED DB: PDB DBREF 4ELT A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4ELT B 101 112 PDB 4ELT 4ELT 101 112 DBREF 4ELT C 201 216 PDB 4ELT 4ELT 201 216 SEQRES 1 A 540 ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY ALA SEQRES 2 A 540 PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET TRP SEQRES 3 A 540 ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY ARG SEQRES 4 A 540 VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG ASP SEQRES 5 A 540 LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SER SEQRES 6 A 540 VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO GLY SEQRES 7 A 540 ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SER SEQRES 8 A 540 ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY GLY SEQRES 9 A 540 GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SER SEQRES 10 A 540 GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU GLY SEQRES 11 A 540 GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU ARG SEQRES 12 A 540 PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR GLY SEQRES 13 A 540 VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER LEU SEQRES 14 A 540 GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU VAL SEQRES 15 A 540 PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER ARG SEQRES 16 A 540 ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY LEU SEQRES 17 A 540 PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SER SEQRES 18 A 540 THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA HIS SEQRES 19 A 540 PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU THR SEQRES 20 A 540 LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP LEU SEQRES 21 A 540 ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE ASN SEQRES 22 A 540 GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER ASP SEQRES 23 A 540 PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU GLY SEQRES 24 A 540 GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY TRP SEQRES 25 A 540 LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU ARG SEQRES 26 A 540 VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE ARG SEQRES 27 A 540 VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR ALA SEQRES 28 A 540 SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP PRO SEQRES 29 A 540 LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY VAL SEQRES 30 A 540 LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU LEU SEQRES 31 A 540 ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU ARG SEQRES 32 A 540 TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE GLU SEQRES 33 A 540 LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL GLU SEQRES 34 A 540 THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU GLU SEQRES 35 A 540 ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG MET SEQRES 36 A 540 ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP LEU SEQRES 37 A 540 MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU GLU SEQRES 38 A 540 GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP GLU SEQRES 39 A 540 LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA VAL SEQRES 40 A 540 ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR PRO SEQRES 41 A 540 LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY GLU SEQRES 42 A 540 ASP TRP LEU SER ALA LYS GLU SEQRES 1 B 12 DG DA DC DC DA DC DG DG DC DG DC DOC SEQRES 1 C 16 DA DA DA DA DG DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC MODRES 4ELT DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC B 112 18 HET 0R5 A 901 38 HET MG A 902 1 HET MG A 903 1 HET GOL A 904 6 HET ACT A 905 4 HET GOL A 906 6 HET GOL A 907 6 HET ACT A 908 4 HET GOL A 909 6 HET GOL A 910 6 HET GOL A 911 6 HET ACT A 912 4 HET GOL A 913 6 HET EDO A 914 4 HET GOL B 201 6 HET GOL C 301 6 HET MG C 302 1 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM 0R5 2'-DEOXY-5-[(4-ETHYNYLPHENYL)ETHYNYL]URIDINE 5'- HETNAM 2 0R5 (TETRAHYDROGEN TRIPHOSPHATE) HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 0R5 C19 H19 N2 O14 P3 FORMUL 5 MG 3(MG 2+) FORMUL 7 GOL 9(C3 H8 O3) FORMUL 8 ACT 3(C2 H3 O2 1-) FORMUL 17 EDO C2 H6 O2 FORMUL 21 HOH *245(H2 O) HELIX 1 1 GLU A 337 LEU A 342 1 6 HELIX 2 2 ARG A 343 LEU A 345 5 3 HELIX 3 3 LEU A 352 GLU A 363 1 12 HELIX 4 4 ASP A 372 ASP A 381 1 10 HELIX 5 5 THR A 386 GLY A 395 1 10 HELIX 6 6 GLU A 401 LEU A 420 1 20 HELIX 7 7 GLU A 423 VAL A 433 1 11 HELIX 8 8 VAL A 433 GLY A 448 1 16 HELIX 9 9 ASP A 452 GLY A 479 1 28 HELIX 10 10 SER A 486 ASP A 496 1 11 HELIX 11 11 SER A 515 LEU A 522 1 8 HELIX 12 12 PRO A 527 TYR A 545 1 19 HELIX 13 13 PRO A 548 ILE A 553 5 6 HELIX 14 14 THR A 588 ARG A 596 1 9 HELIX 15 15 GLN A 613 GLY A 624 1 12 HELIX 16 16 ASP A 625 GLU A 634 1 10 HELIX 17 17 ASP A 637 GLY A 648 1 12 HELIX 18 18 PRO A 650 VAL A 654 5 5 HELIX 19 19 ASP A 655 TYR A 671 1 17 HELIX 20 20 SER A 674 ALA A 683 1 10 HELIX 21 21 PRO A 685 PHE A 700 1 16 HELIX 22 22 PRO A 701 GLY A 718 1 18 HELIX 23 23 PRO A 731 ALA A 735 5 5 HELIX 24 24 VAL A 737 GLY A 776 1 40 HELIX 25 25 ARG A 795 GLY A 809 1 15 HELIX 26 26 ASP A 826 LYS A 831 1 6 SHEET 1 A 4 GLU A 295 ALA A 297 0 SHEET 2 A 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 A 4 LEU A 321 ALA A 327 -1 N ALA A 326 O HIS A 333 SHEET 4 A 4 PHE A 306 LEU A 311 -1 N GLY A 308 O ALA A 325 SHEET 1 B 2 ARG A 450 LEU A 451 0 SHEET 2 B 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 C 2 ARG A 563 ASN A 565 0 SHEET 2 C 2 SER A 575 SER A 577 -1 O SER A 577 N ARG A 563 SHEET 1 D 4 ARG A 778 GLN A 782 0 SHEET 2 D 4 GLU A 786 PRO A 792 -1 O VAL A 788 N LEU A 781 SHEET 3 D 4 TRP A 604 TYR A 611 -1 N VAL A 607 O LEU A 789 SHEET 4 D 4 VAL A 819 GLY A 824 -1 O GLU A 820 N ASP A 610 SHEET 1 E 2 TYR A 719 GLU A 721 0 SHEET 2 E 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK O3' DC B 111 P DOC B 112 1555 1555 1.61 LINK OD1 ASP A 610 MG MG A 902 1555 1555 2.19 LINK OD2 ASP A 610 MG MG A 903 1555 1555 2.50 LINK O TYR A 611 MG MG A 902 1555 1555 2.12 LINK OD2 ASP A 785 MG MG A 902 1555 1555 2.15 LINK OD1 ASP A 785 MG MG A 903 1555 1555 2.18 LINK O2G 0R5 A 901 MG MG A 902 1555 1555 1.99 LINK O2B 0R5 A 901 MG MG A 902 1555 1555 2.20 LINK O1A 0R5 A 901 MG MG A 902 1555 1555 2.23 LINK O1A 0R5 A 901 MG MG A 903 1555 1555 2.38 LINK MG MG A 903 O HOH A1001 1555 1555 2.53 LINK MG MG A 903 O HOH A1002 1555 1555 2.76 LINK MG MG C 302 O HOH C 432 1555 1555 2.05 LINK MG MG C 302 O HOH C 433 1555 1555 2.15 LINK MG MG C 302 O HOH C 434 1555 1555 2.16 LINK MG MG C 302 O HOH C 435 1555 1555 2.15 CISPEP 1 TRP A 299 PRO A 300 0 0.79 CISPEP 2 ASP A 578 PRO A 579 0 -1.53 SITE 1 AC1 27 ARG A 573 ARG A 587 ASP A 610 TYR A 611 SITE 2 AC1 27 SER A 612 GLN A 613 ILE A 614 GLU A 615 SITE 3 AC1 27 HIS A 639 ARG A 659 ARG A 660 LYS A 663 SITE 4 AC1 27 THR A 664 PHE A 667 ASP A 785 MG A 902 SITE 5 AC1 27 MG A 903 HOH A1002 HOH A1006 HOH A1056 SITE 6 AC1 27 HOH A1066 HOH A1067 HOH A1084 HOH A1115 SITE 7 AC1 27 DOC B 112 DA C 204 DG C 205 SITE 1 AC2 5 ASP A 610 TYR A 611 ASP A 785 0R5 A 901 SITE 2 AC2 5 MG A 903 SITE 1 AC3 7 ASP A 610 ASP A 785 0R5 A 901 MG A 902 SITE 2 AC3 7 HOH A1001 HOH A1002 DOC B 112 SITE 1 AC4 6 ARG A 660 LYS A 663 LYS A 831 HOH A1067 SITE 2 AC4 6 HOH A1115 DOC B 112 SITE 1 AC5 4 ASP A 452 TYR A 455 ARG A 596 ASP A 826 SITE 1 AC6 4 GLY A 672 GLU A 745 ARG A 746 DA C 203 SITE 1 AC7 9 THR A 544 TYR A 545 PRO A 579 ASN A 580 SITE 2 AC7 9 ASN A 583 GOL A 910 HOH A1136 DC C 209 SITE 3 AC7 9 DC C 210 SITE 1 AC8 3 ARG A 313 TRP A 318 ASP A 551 SITE 1 AC9 7 LYS A 354 ASP A 355 ARG A 563 GLN A 566 SITE 2 AC9 7 HOH A1009 HOH A1073 HOH A1128 SITE 1 BC1 7 LEU A 552 ASP A 578 PRO A 579 GOL A 907 SITE 2 BC1 7 HOH A1018 DC C 209 DC C 210 SITE 1 BC2 7 LYS A 508 THR A 509 ARG A 715 LEU A 733 SITE 2 BC2 7 GLU A 734 ARG A 736 HOH A1134 SITE 1 BC3 2 SER A 460 LYS A 542 SITE 1 BC4 4 ARG A 728 TYR A 729 HOH A1013 HOH A1173 SITE 1 BC5 4 GLU A 347 ARG A 349 GLY A 370 ASP A 371 SITE 1 BC6 8 DG B 107 DG B 108 HOH B 313 HOH B 315 SITE 2 BC6 8 HOH B 323 DG C 208 DC C 209 HOH C 416 SITE 1 BC7 4 ARG A 728 HOH A1173 DG C 206 DC C 207 SITE 1 BC8 4 HOH C 432 HOH C 433 HOH C 434 HOH C 435 CRYST1 108.860 108.860 91.004 90.00 90.00 120.00 P 31 2 1 6 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 0.009186 0.005304 0.000000 0.00000 SCALE2 0.000000 0.010607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010989 0.00000