HEADER TRANSFERASE/DNA 23-AUG-10 3OJU TITLE SNAPSHOT OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS TITLE 2 AQUATICUS PROCESSING C5 MODIFIED THYMIDIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 292-832; COMPND 5 SYNONYM: TAQ POLYMERASE 1; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DNA PRIMER; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- COMPND 15 3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES; COMPND 18 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-21B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS DNA POLYMERASE, C5 MODIFIED NUCLEOTIDE ANALOGS, BINDING POCKET, SPIN- KEYWDS 2 LABELED TRIPHOSPHATE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MARX,K.DIEDERICHS,S.OBEID REVDAT 3 08-NOV-17 3OJU 1 REMARK REVDAT 2 27-MAR-13 3OJU 1 JRNL VERSN REVDAT 1 15-DEC-10 3OJU 0 JRNL AUTH S.OBEID,A.BACCARO,W.WELTE,K.DIEDERICHS,A.MARX JRNL TITL STRUCTURAL BASIS FOR THE SYNTHESIS OF NUCLEOBASE MODIFIED JRNL TITL 2 DNA BY THERMUS AQUATICUS DNA POLYMERASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 21327 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 21123743 JRNL DOI 10.1073/PNAS.1013804107 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.1 REMARK 3 NUMBER OF REFLECTIONS : 32113 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 1664 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 47.2210 - 4.5775 1.00 3541 189 0.2025 0.2368 REMARK 3 2 4.5775 - 3.6337 1.00 3389 203 0.1508 0.1896 REMARK 3 3 3.6337 - 3.1745 0.99 3382 191 0.1549 0.1819 REMARK 3 4 3.1745 - 2.8843 0.99 3370 173 0.1666 0.2194 REMARK 3 5 2.8843 - 2.6776 0.99 3340 180 0.1828 0.2462 REMARK 3 6 2.6776 - 2.5197 0.99 3314 187 0.1850 0.2305 REMARK 3 7 2.5197 - 2.3935 0.86 2895 150 0.1987 0.2461 REMARK 3 8 2.3935 - 2.2894 0.65 2177 104 0.1814 0.2727 REMARK 3 9 2.2894 - 2.2012 0.51 1733 97 0.1906 0.2802 REMARK 3 10 2.2012 - 2.1253 0.41 1362 77 0.2076 0.2625 REMARK 3 11 2.1253 - 2.0588 0.33 1090 63 0.2169 0.2761 REMARK 3 12 2.0588 - 2.0000 0.26 856 50 0.2228 0.2563 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 : 0.44 REMARK 3 B_SOL : 53.65 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.75360 REMARK 3 B22 (A**2) : 0.75360 REMARK 3 B33 (A**2) : -1.50730 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 : 0.004 5081 REMARK 3 ANGLE : 1.060 6962 REMARK 3 CHIRALITY : 0.053 758 REMARK 3 PLANARITY : 0.004 806 REMARK 3 DIHEDRAL : 17.586 1980 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 295:627) REMARK 3 ORIGIN FOR THE GROUP (A): 36.0523 -25.9673 -9.0621 REMARK 3 T TENSOR REMARK 3 T11: 0.1932 T22: 0.1622 REMARK 3 T33: 0.1612 T12: -0.0296 REMARK 3 T13: 0.0381 T23: 0.0158 REMARK 3 L TENSOR REMARK 3 L11: 0.3985 L22: 0.5426 REMARK 3 L33: 0.8020 L12: 0.2153 REMARK 3 L13: -0.0068 L23: 0.0058 REMARK 3 S TENSOR REMARK 3 S11: -0.0317 S12: -0.0353 S13: -0.0482 REMARK 3 S21: -0.1871 S22: -0.0120 S23: -0.0877 REMARK 3 S31: -0.0591 S32: -0.0083 S33: 0.0346 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 628:697) REMARK 3 ORIGIN FOR THE GROUP (A): 8.2238 -12.3281 -3.0464 REMARK 3 T TENSOR REMARK 3 T11: 0.8258 T22: 0.5537 REMARK 3 T33: 0.2329 T12: 0.3328 REMARK 3 T13: 0.0308 T23: -0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.9937 L22: 1.0166 REMARK 3 L33: 0.4986 L12: 0.2437 REMARK 3 L13: -0.6450 L23: -0.4265 REMARK 3 S TENSOR REMARK 3 S11: -0.0410 S12: -0.2050 S13: 0.2604 REMARK 3 S21: 1.0274 S22: 0.2115 S23: 0.1848 REMARK 3 S31: -0.5341 S32: -0.0527 S33: -0.1475 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 698:832) REMARK 3 ORIGIN FOR THE GROUP (A): 18.7824 -25.9696 -14.9887 REMARK 3 T TENSOR REMARK 3 T11: 0.2508 T22: 0.2910 REMARK 3 T33: 0.1850 T12: -0.0180 REMARK 3 T13: 0.0053 T23: 0.0205 REMARK 3 L TENSOR REMARK 3 L11: 0.3543 L22: 0.3042 REMARK 3 L33: 1.4033 L12: -0.1665 REMARK 3 L13: 0.2943 L23: 0.2870 REMARK 3 S TENSOR REMARK 3 S11: -0.0157 S12: 0.1073 S13: -0.0151 REMARK 3 S21: -0.0970 S22: 0.0483 S23: 0.0732 REMARK 3 S31: -0.2414 S32: -0.4020 S33: -0.0306 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 101:112) REMARK 3 ORIGIN FOR THE GROUP (A): 37.2588 -22.9889 4.5321 REMARK 3 T TENSOR REMARK 3 T11: 0.1636 T22: 0.2289 REMARK 3 T33: 0.2026 T12: 0.0274 REMARK 3 T13: -0.0424 T23: -0.0361 REMARK 3 L TENSOR REMARK 3 L11: 3.3483 L22: 0.4211 REMARK 3 L33: 0.4573 L12: -0.0370 REMARK 3 L13: -0.3602 L23: 0.3623 REMARK 3 S TENSOR REMARK 3 S11: -0.0807 S12: 0.2107 S13: -0.2880 REMARK 3 S21: -0.0827 S22: 0.0748 S23: 0.0047 REMARK 3 S31: -0.2619 S32: 0.4475 S33: -0.0062 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN C AND RESID 203:216) REMARK 3 ORIGIN FOR THE GROUP (A): 34.7239 -24.1738 5.6957 REMARK 3 T TENSOR REMARK 3 T11: 0.1544 T22: 0.1613 REMARK 3 T33: 0.1626 T12: 0.0569 REMARK 3 T13: -0.0129 T23: 0.0395 REMARK 3 L TENSOR REMARK 3 L11: 2.1913 L22: 0.7383 REMARK 3 L33: 1.5101 L12: 1.0138 REMARK 3 L13: 0.2304 L23: 0.1795 REMARK 3 S TENSOR REMARK 3 S11: -0.3643 S12: 0.1350 S13: -0.2087 REMARK 3 S21: -0.0824 S22: 0.2526 S23: -0.1040 REMARK 3 S31: -0.1378 S32: 0.0156 S33: 0.0766 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 3OJU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000061206. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 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) : 1.0000 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR WITH DUAL REMARK 200 CHANNEL CUT CRYSTALS AND A REMARK 200 TOROIDAL MIRROR (M2) REMARK 200 OPTICS : VERTICALLY COLLIMATING MIRROR REMARK 200 (M1, FOCUS AT INFINITY), REMARK 200 FOLLOWED BY BARTELS REMARK 200 MONOCHROMATOR WITH DUAL CHANNEL REMARK 200 CUT CRYSTALS 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 : 32113 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 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 (%) : 74.5 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 28.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.840 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.6.4_486 REMARK 200 STARTING MODEL: PDB ENTRY 3M8R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M TRIS HCL PH 9, 0.2M NH4CL, 0.01M REMARK 280 CACL2, 26% PEG 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K 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 30.49100 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 60.98200 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 60.98200 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 30.49100 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: 9170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 A 131 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 465 DA C 201 REMARK 465 DA C 202 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. = 2.4 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 111 C3' - O3' - P ANGL. DEV. = -13.8 DEGREES REMARK 500 DOC B 112 O3' - P - OP2 ANGL. DEV. = 9.0 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 1.9 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 ASP A 381 110.85 -165.79 REMARK 500 THR A 399 -169.38 -110.04 REMARK 500 VAL A 433 -68.65 -121.24 REMARK 500 TYR A 545 -56.35 -125.01 REMARK 500 ASP A 578 48.82 71.09 REMARK 500 VAL A 586 -15.29 -159.70 REMARK 500 GLN A 613 48.53 38.28 REMARK 500 VAL A 654 93.16 -161.89 REMARK 500 GLN A 680 44.28 -95.96 REMARK 500 GLU A 681 -37.39 -136.05 REMARK 500 LEU A 682 -77.83 -113.82 REMARK 500 ALA A 683 -137.82 -176.96 REMARK 500 GLU A 687 -17.99 73.98 REMARK 500 ASP A 732 3.06 -68.15 REMARK 500 HIS A 784 -69.32 72.42 REMARK 500 TYR A 811 92.36 -165.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PGE A 7 REMARK 610 PGE A 8 REMARK 610 PGE A 10 REMARK 610 PGE A 11 REMARK 610 PGE A 12 REMARK 610 PGE A 13 REMARK 610 PGE A 14 REMARK 610 PGE A 16 REMARK 610 PGE A 17 REMARK 610 PGE A 18 REMARK 610 PGE C 2 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 2 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SSJ A 1 O1G REMARK 620 2 TYR A 611 O 106.2 REMARK 620 3 ASP A 785 OD2 159.3 88.3 REMARK 620 4 SSJ A 1 O1B 72.1 96.2 92.0 REMARK 620 5 ASP A 610 OD1 100.5 87.6 94.7 172.4 REMARK 620 6 SSJ A 1 O2A 80.5 161.4 81.4 68.8 108.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 3 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 HOH A 33 O 123.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SSJ A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 10 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 12 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 14 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 15 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 16 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 17 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 18 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE C 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OJS RELATED DB: PDB REMARK 900 RELATED ID: 3LWL RELATED DB: PDB REMARK 900 RELATED ID: 3LWM RELATED DB: PDB REMARK 900 RELATED ID: 3M8R RELATED DB: PDB REMARK 900 RELATED ID: 3M8S RELATED DB: PDB DBREF 3OJU A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 3OJU B 101 112 PDB 3OJU 3OJU 101 112 DBREF 3OJU C 201 216 PDB 3OJU 3OJU 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 3OJU DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC B 112 30 HET SSJ A 1 40 HET MG A 2 1 HET MG A 3 1 HET GOL A 4 14 HET GOL A 5 14 HET GOL A 6 14 HET PGE A 7 8 HET PGE A 8 8 HET GOL A 9 14 HET PGE A 10 8 HET PGE A 11 8 HET PGE A 12 10 HET PGE A 13 8 HET PGE A 14 8 HET GOL A 15 14 HET PGE A 16 8 HET PGE A 17 8 HET PGE A 18 8 HET GOL C 1 14 HET PGE C 2 17 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM SSJ 2'-DEOXY-5-[(1-HYDROXY-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO- HETNAM 2 SSJ 1H-PYRROL-3-YL)ETHYNYL]URIDINE 5'-(TETRAHYDROGEN HETNAM 3 SSJ TRIPHOSPHATE) HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM PGE TRIETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 SSJ C19 H28 N3 O15 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 GOL 6(C3 H8 O3) FORMUL 10 PGE 11(C6 H14 O4) FORMUL 24 HOH *195(H2 O) HELIX 1 1 GLU A 337 ARG A 343 1 7 HELIX 2 2 LEU A 352 GLU A 363 1 12 HELIX 3 3 ASP A 372 ASP A 381 1 10 HELIX 4 4 THR A 386 GLY A 395 1 10 HELIX 5 5 GLU A 401 GLY A 422 1 22 HELIX 6 6 GLU A 423 VAL A 433 1 11 HELIX 7 7 VAL A 433 GLY A 448 1 16 HELIX 8 8 ASP A 452 GLY A 479 1 28 HELIX 9 9 SER A 486 ASP A 496 1 11 HELIX 10 10 SER A 515 LEU A 522 1 8 HELIX 11 11 PRO A 527 TYR A 545 1 19 HELIX 12 12 PRO A 548 ILE A 553 5 6 HELIX 13 13 THR A 588 ARG A 596 1 9 HELIX 14 14 GLN A 613 GLY A 624 1 12 HELIX 15 15 ASP A 625 GLU A 634 1 10 HELIX 16 16 ASP A 637 GLY A 648 1 12 HELIX 17 17 ASP A 655 TYR A 671 1 17 HELIX 18 18 SER A 674 GLN A 680 1 7 HELIX 19 19 ALA A 689 PHE A 700 1 12 HELIX 20 20 PHE A 700 GLY A 718 1 19 HELIX 21 21 PRO A 731 ALA A 735 5 5 HELIX 22 22 VAL A 737 GLY A 776 1 40 HELIX 23 23 ARG A 795 GLY A 809 1 15 HELIX 24 24 ASP A 826 LYS A 831 1 6 SHEET 1 A 4 GLU A 295 PRO A 298 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 ARG A 328 -1 N ALA A 326 O HIS A 333 SHEET 4 A 4 PHE A 306 LEU A 311 -1 N PHE A 306 O ALA A 327 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 575 N ASN A 565 SHEET 1 D 4 ARG A 778 GLN A 782 0 SHEET 2 D 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 D 4 TRP A 604 TYR A 611 -1 N LEU A 609 O LEU A 787 SHEET 4 D 4 VAL A 819 GLY A 824 -1 O GLY A 824 N LEU A 606 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 1.60 LINK O1G SSJ A 1 MG MG A 2 1555 1555 2.23 LINK O TYR A 611 MG MG A 2 1555 1555 2.27 LINK OD2 ASP A 785 MG MG A 2 1555 1555 2.29 LINK O1B SSJ A 1 MG MG A 2 1555 1555 2.30 LINK OD1 ASP A 610 MG MG A 2 1555 1555 2.34 LINK O2A SSJ A 1 MG MG A 2 1555 1555 2.45 LINK OD2 ASP A 610 MG MG A 3 1555 1555 2.65 LINK MG MG A 3 O HOH A 33 1555 1555 2.70 CISPEP 1 TRP A 299 PRO A 300 0 6.68 CISPEP 2 ASP A 578 PRO A 579 0 0.29 CISPEP 3 PRO A 685 TYR A 686 0 -12.68 SITE 1 AC1 24 MG A 2 MG A 3 HOH A 33 HOH A 70 SITE 2 AC1 24 HOH A 126 ARG A 573 ARG A 587 ASP A 610 SITE 3 AC1 24 TYR A 611 SER A 612 GLN A 613 ILE A 614 SITE 4 AC1 24 GLU A 615 HIS A 639 ARG A 659 ARG A 660 SITE 5 AC1 24 LYS A 663 THR A 664 PHE A 667 ASP A 785 SITE 6 AC1 24 DC B 111 DOC B 112 DA C 204 DG C 205 SITE 1 AC2 4 SSJ A 1 ASP A 610 TYR A 611 ASP A 785 SITE 1 AC3 4 SSJ A 1 HOH A 33 ASP A 610 ASP A 785 SITE 1 AC4 5 HOH A 163 LYS A 354 ASP A 355 ASN A 565 SITE 2 AC4 5 GLN A 566 SITE 1 AC5 7 THR A 544 PRO A 579 ASN A 580 ASN A 583 SITE 2 AC5 7 HOH C 22 DC C 209 DC C 210 SITE 1 AC6 6 GOL A 9 HOH A 157 ASN A 485 DG B 107 SITE 2 AC6 6 DG C 211 DT C 212 SITE 1 AC7 4 GLU A 347 ARG A 349 GLY A 370 ASP A 371 SITE 1 AC8 2 GLU A 745 ARG A 746 SITE 1 AC9 9 GOL A 6 ASN A 485 SER A 486 ARG A 487 SITE 2 AC9 9 ASP A 488 HOH B 31 DG C 211 DT C 212 SITE 3 AC9 9 DG C 213 SITE 1 BC1 5 HOH A 42 HOH A 131 LYS A 767 ARG A 771 SITE 2 BC1 5 VAL A 810 SITE 1 BC2 2 ASP A 371 ARG A 435 SITE 1 BC3 4 ARG A 313 GLU A 315 TRP A 318 LEU A 552 SITE 1 BC4 4 GLY A 396 GLU A 397 GLU A 404 ARG A 411 SITE 1 BC5 2 SER A 460 LYS A 542 SITE 1 BC6 3 ARG A 425 TRP A 428 PHE A 724 SITE 1 BC7 2 THR A 447 ARG A 778 SITE 1 BC8 1 GLY A 479 SITE 1 BC9 5 HOH A 124 LYS A 508 THR A 509 GLU A 734 SITE 2 BC9 5 ALA A 735 SITE 1 CC1 5 ARG A 728 MET A 747 PGE C 2 DG C 206 SITE 2 CC1 5 DC C 207 SITE 1 CC2 5 GOL C 1 HOH C 31 DG C 205 DG C 206 SITE 2 CC2 5 DC C 207 CRYST1 109.022 109.022 91.473 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 0.009172 0.005296 0.000000 0.00000 SCALE2 0.000000 0.010591 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010932 0.00000 MASTER 494 0 21 24 14 0 34 6 0 0 0 45 END