HEADER TRANSFERASE/DNA 11-APR-12 4ELV 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 FRAGMENT: UNP RESIDUES 293-832; 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*(0R8))-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*GP*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: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 OTHER_DETAILS: DNA SYNTHESIZER; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 OTHER_DETAILS: DNA SYNTHESIZER KEYWDS DNA POLYMERASE, MODIFIED NUCLEOTIDES, A FAMILY, DNA SYNTHESIS, RIGID KEYWDS 2 LINKER, ELONGATION OF MODIFIED DNA, NON-NATURAL NUCLEOTIDE, KEYWDS 3 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MARX,K.DIEDERICHS,S.OBEID REVDAT 2 13-SEP-23 4ELV 1 REMARK LINK REVDAT 1 24-APR-13 4ELV 0 JRNL AUTH S.OBEID,H.BU KAMP,W.WELTE,K.DIEDERICHS,A.MARX JRNL TITL SNAPSHOT OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM JRNL TITL 2 THERMUS AQUATICUS PROCESSING MODIFIED PYRIMIDINES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1009) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 49722 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 : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2491 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 47.3052 - 4.9776 1.00 2778 157 0.1739 0.1915 REMARK 3 2 4.9776 - 3.9515 1.00 2671 141 0.1391 0.1811 REMARK 3 3 3.9515 - 3.4522 1.00 2644 155 0.1426 0.1787 REMARK 3 4 3.4522 - 3.1366 1.00 2615 150 0.1624 0.1881 REMARK 3 5 3.1366 - 2.9118 1.00 2640 132 0.1786 0.2613 REMARK 3 6 2.9118 - 2.7402 1.00 2625 138 0.1869 0.2226 REMARK 3 7 2.7402 - 2.6030 1.00 2604 148 0.1736 0.2299 REMARK 3 8 2.6030 - 2.4897 1.00 2611 146 0.1703 0.2190 REMARK 3 9 2.4897 - 2.3938 1.00 2627 129 0.1735 0.2256 REMARK 3 10 2.3938 - 2.3112 1.00 2625 118 0.1782 0.2380 REMARK 3 11 2.3112 - 2.2389 1.00 2616 142 0.1986 0.2593 REMARK 3 12 2.2389 - 2.1749 1.00 2607 120 0.2042 0.2475 REMARK 3 13 2.1749 - 2.1177 1.00 2591 122 0.2056 0.2300 REMARK 3 14 2.1177 - 2.0660 1.00 2607 143 0.2123 0.2428 REMARK 3 15 2.0660 - 2.0191 1.00 2568 126 0.2303 0.2411 REMARK 3 16 2.0191 - 1.9761 1.00 2622 152 0.2421 0.3034 REMARK 3 17 1.9761 - 1.9366 1.00 2598 141 0.2523 0.2869 REMARK 3 18 1.9366 - 1.9000 1.00 2582 131 0.2918 0.3147 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 : 0.86 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 42.09 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.520 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) : 5.15870 REMARK 3 B22 (A**2) : 5.15870 REMARK 3 B33 (A**2) : -5.12260 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 5091 REMARK 3 ANGLE : 1.172 7016 REMARK 3 CHIRALITY : 0.071 757 REMARK 3 PLANARITY : 0.005 815 REMARK 3 DIHEDRAL : 16.929 1991 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 294:452) REMARK 3 ORIGIN FOR THE GROUP (A): 39.6541 -41.3099 -18.1133 REMARK 3 T TENSOR REMARK 3 T11: 0.2428 T22: 0.1800 REMARK 3 T33: 0.2399 T12: -0.0703 REMARK 3 T13: 0.0536 T23: -0.0189 REMARK 3 L TENSOR REMARK 3 L11: 1.2952 L22: 2.4057 REMARK 3 L33: 1.3023 L12: -0.2787 REMARK 3 L13: 0.1009 L23: -0.0531 REMARK 3 S TENSOR REMARK 3 S11: 0.0377 S12: 0.0541 S13: -0.2548 REMARK 3 S21: -0.2331 S22: -0.0078 S23: -0.3006 REMARK 3 S31: 0.2021 S32: 0.0983 S33: -0.0092 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 453:603) REMARK 3 ORIGIN FOR THE GROUP (A): 35.9605 -11.0648 1.7800 REMARK 3 T TENSOR REMARK 3 T11: 0.2221 T22: 0.1130 REMARK 3 T33: 0.1890 T12: -0.0289 REMARK 3 T13: 0.0092 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 1.1722 L22: 2.0252 REMARK 3 L33: 2.2516 L12: 0.8312 REMARK 3 L13: 0.0420 L23: 0.4162 REMARK 3 S TENSOR REMARK 3 S11: 0.0082 S12: -0.0791 S13: 0.1730 REMARK 3 S21: 0.0045 S22: -0.0499 S23: 0.0883 REMARK 3 S31: -0.5206 S32: -0.0101 S33: 0.0310 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 604:832) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0479 -21.5823 -11.6594 REMARK 3 T TENSOR REMARK 3 T11: 0.2502 T22: 0.4563 REMARK 3 T33: 0.2241 T12: 0.1159 REMARK 3 T13: 0.0155 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 1.9040 L22: 1.6450 REMARK 3 L33: 3.8707 L12: 0.7345 REMARK 3 L13: 0.2599 L23: -1.2652 REMARK 3 S TENSOR REMARK 3 S11: -0.0830 S12: -0.1555 S13: 0.2592 REMARK 3 S21: -0.0181 S22: 0.1950 S23: 0.3561 REMARK 3 S31: -0.7083 S32: -1.1199 S33: -0.1221 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 4ELV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA 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 : LN2 COOLED FIXED-EXIT, SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR, LN2 REMARK 200 COOLED FIXED-EXIT, SI(111) REMARK 200 MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50305 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.11800 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) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.18200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX DEV_1009 REMARK 200 STARTING MODEL: PDB ENTRY 3OJS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS HCL PH=8.4, 0.2 M NH4CL, 10 REMARK 280 MM CACL2, 34% PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K, PH 8.4 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 30.34900 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 60.69800 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 60.69800 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 30.34900 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: 6950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 A1175 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1191 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1205 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1227 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 465 DA C 203 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 O10 0R7 A 902 O HOH A 1200 2.16 REMARK 500 OE1 GLU A 708 O HOH A 1166 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC C 210 O3' DC C 210 C3' -0.038 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 DA B 102 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA B 105 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC B 106 O4' - C1' - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 DC B 111 C3' - O3' - P ANGL. DEV. = -16.2 DEGREES REMARK 500 0R8 B 112 O3' - P - OP2 ANGL. DEV. = 12.2 DEGREES REMARK 500 0R8 B 112 O3' - P - OP1 ANGL. DEV. = -17.5 DEGREES REMARK 500 DG C 204 OP1 - P - OP2 ANGL. DEV. = -11.3 DEGREES REMARK 500 DT C 212 O4' - C1' - N1 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 3.0 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 381 108.64 -167.08 REMARK 500 VAL A 433 -68.45 -122.54 REMARK 500 TYR A 545 -57.47 -122.95 REMARK 500 VAL A 586 -19.20 -154.94 REMARK 500 PRO A 650 -70.63 -45.55 REMARK 500 ARG A 651 -31.09 178.21 REMARK 500 HIS A 784 -67.08 71.98 REMARK 500 TYR A 811 96.41 -161.35 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 904 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 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 GLU A 786 OE2 89.2 REMARK 620 3 HOH A1019 O 158.8 89.4 REMARK 620 4 HOH A1048 O 91.9 152.8 79.9 REMARK 620 5 HOH A1129 O 74.9 84.4 83.9 69.8 REMARK 620 6 HOH A1196 O 95.5 87.8 105.6 119.1 167.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 908 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 78.7 REMARK 620 3 ASP A 785 OD2 90.5 91.1 REMARK 620 4 0R7 A 902 O7 95.1 95.6 172.0 REMARK 620 5 0R7 A 902 O9 165.3 88.6 97.2 78.7 REMARK 620 6 0R7 A 902 O11 114.2 166.7 85.9 86.6 79.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 335 O REMARK 620 2 HOH B 336 O 179.1 REMARK 620 3 HOH B 337 O 87.7 91.5 REMARK 620 4 HOH B 338 O 91.5 88.6 118.7 REMARK 620 5 HOH C 437 O 89.9 90.9 170.7 52.3 REMARK 620 6 HOH C 444 O 89.7 91.0 119.3 121.9 69.6 REMARK 620 N 1 2 3 4 5 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 439 O REMARK 620 2 HOH C 440 O 179.4 REMARK 620 3 HOH C 441 O 90.3 90.2 REMARK 620 4 HOH C 442 O 90.4 89.6 119.5 REMARK 620 5 HOH C 443 O 91.1 88.3 119.8 120.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0R7 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL 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 EDO A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 303 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: 4ELT RELATED DB: PDB REMARK 900 RELATED ID: 4ELU RELATED DB: PDB DBREF 4ELV A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4ELV B 101 112 PDB 4ELV 4ELV 101 112 DBREF 4ELV C 201 216 PDB 4ELV 4ELV 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 0R8 SEQRES 1 C 16 DA DA DA DG DG DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC MODRES 4ELV 0R8 B 112 DC HET 0R8 B 112 28 HET MG A 901 1 HET 0R7 A 902 37 HET GOL A 903 6 HET PGE A 904 4 HET GOL A 905 6 HET GOL A 906 6 HET EDO A 907 4 HET CA A 908 1 HET MG B 201 1 HET GOL C 301 6 HET MG C 302 1 HET EDO C 303 4 HETNAM 0R8 [(2S,5R)-5-{4-AMINO-5-[(4-ETHYNYLPHENYL)ETHYNYL]-2- HETNAM 2 0R8 OXOPYRIMIDIN-1(2H)-YL}TETRAHYDROFURAN-2-YL]METHYL HETNAM 3 0R8 DIHYDROGEN PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM 0R7 [[(2S,5R)-5-[4-AZANYL-5-[2-(4-ETHYNYLPHENYL)ETHYNYL]-2- HETNAM 2 0R7 OXIDANYLIDENE-PYRIMIDIN-1-YL]OXOLAN-2-YL]METHOXY- HETNAM 3 0R7 OXIDANYL-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE HETNAM GOL GLYCEROL HETNAM PGE TRIETHYLENE GLYCOL HETNAM EDO 1,2-ETHANEDIOL HETNAM CA CALCIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 0R8 C19 H18 N3 O6 P FORMUL 4 MG 3(MG 2+) FORMUL 5 0R7 C19 H20 N3 O12 P3 FORMUL 6 GOL 4(C3 H8 O3) FORMUL 7 PGE C6 H14 O4 FORMUL 10 EDO 2(C2 H6 O2) FORMUL 11 CA CA 2+ FORMUL 16 HOH *323(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 LEU A 420 1 20 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 ALA A 683 1 10 HELIX 19 19 PRO A 685 PHE A 700 1 16 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 MET A 775 1 39 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 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 ARG A 328 -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 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 VAL A 607 O LEU A 789 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 0R8 B 112 1555 1555 1.61 LINK OD2 ASP A 610 MG MG A 901 1555 1555 2.15 LINK OD1 ASP A 610 CA CA A 908 1555 1555 2.40 LINK O TYR A 611 CA CA A 908 1555 1555 2.28 LINK OD2 ASP A 785 CA CA A 908 1555 1555 2.28 LINK OE2AGLU A 786 MG MG A 901 1555 1555 2.10 LINK MG MG A 901 O HOH A1019 1555 1555 2.15 LINK MG MG A 901 O HOH A1048 1555 1555 2.08 LINK MG MG A 901 O HOH A1129 1555 1555 2.10 LINK MG MG A 901 O HOH A1196 1555 1555 2.03 LINK O7 0R7 A 902 CA CA A 908 1555 1555 2.26 LINK O9 0R7 A 902 CA CA A 908 1555 1555 2.32 LINK O11 0R7 A 902 CA CA A 908 1555 1555 2.41 LINK MG MG B 201 O HOH B 335 1555 1555 2.18 LINK MG MG B 201 O HOH B 336 1555 1555 2.18 LINK MG MG B 201 O HOH B 337 1555 1555 2.16 LINK MG MG B 201 O HOH B 338 1555 1555 2.18 LINK MG MG B 201 O HOH C 437 1555 1555 2.95 LINK MG MG B 201 O HOH C 444 1555 1555 2.18 LINK MG MG C 302 O HOH C 439 1555 1555 2.18 LINK MG MG C 302 O HOH C 440 1555 1555 2.18 LINK MG MG C 302 O HOH C 441 1555 1555 2.18 LINK MG MG C 302 O HOH C 442 1555 1555 2.18 LINK MG MG C 302 O HOH C 443 1555 1555 2.18 CISPEP 1 TRP A 299 PRO A 300 0 1.62 CISPEP 2 ASP A 578 PRO A 579 0 2.48 SITE 1 AC1 7 ASP A 610 GLU A 786 0R7 A 902 HOH A1019 SITE 2 AC1 7 HOH A1048 HOH A1129 HOH A1196 SITE 1 AC2 24 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC2 24 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC2 24 ARG A 659 ARG A 660 LYS A 663 PHE A 667 SITE 4 AC2 24 ASP A 785 MG A 901 CA A 908 HOH A1045 SITE 5 AC2 24 HOH A1080 HOH A1196 HOH A1200 HOH A1207 SITE 6 AC2 24 HOH A1231 0R8 B 112 DG C 204 DG C 205 SITE 1 AC3 10 THR A 544 TYR A 545 PRO A 579 ASN A 580 SITE 2 AC3 10 ASN A 583 HOH A1090 HOH A1155 DC C 209 SITE 3 AC3 10 DC C 210 HOH C 405 SITE 1 AC4 4 ASP A 371 TRP A 417 ARG A 431 ARG A 435 SITE 1 AC5 7 ARG A 425 LEU A 723 PHE A 724 GLU A 774 SITE 2 AC5 7 TYR A 811 HOH A1160 HOH A1239 SITE 1 AC6 6 ASP A 452 TYR A 455 ARG A 593 ARG A 596 SITE 2 AC6 6 ILE A 599 HOH A1110 SITE 1 AC7 3 LEU A 311 GLU A 400 ARG A 405 SITE 1 AC8 4 ASP A 610 TYR A 611 ASP A 785 0R7 A 902 SITE 1 AC9 6 HOH B 335 HOH B 336 HOH B 337 HOH B 338 SITE 2 AC9 6 HOH C 437 HOH C 444 SITE 1 BC1 5 DG C 205 DG C 206 HOH C 404 HOH C 426 SITE 2 BC1 5 HOH C 429 SITE 1 BC2 6 DG C 214 HOH C 439 HOH C 440 HOH C 441 SITE 2 BC2 6 HOH C 442 HOH C 443 SITE 1 BC3 4 ALA A 570 ARG A 728 DG C 206 DC C 207 CRYST1 109.213 109.213 91.047 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 0.009156 0.005286 0.000000 0.00000 SCALE2 0.000000 0.010573 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010983 0.00000