HEADER TRANSFERASE/DNA 23-AUG-10 3OJS TITLE SNAPSHOTS OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS TITLE 2 AQUATICUS PROCESSING C5 MODIFIED THYMIDINES 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 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE KEYWDS DNA POLYMERASE, C5 MODIFIED NUCLEOTIDE ANALOGS, BINDING POCKET, KEYWDS 2 DENRON-LABELED TRIPHOSPHATE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MARX,K.DIEDERICHS,S.OBEID REVDAT 4 06-SEP-23 3OJS 1 REMARK LINK REVDAT 3 08-NOV-17 3OJS 1 REMARK REVDAT 2 27-MAR-13 3OJS 1 JRNL VERSN REVDAT 1 15-DEC-10 3OJS 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. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 47553 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2401 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 46.7054 - 4.8837 1.00 2833 161 0.1745 0.2082 REMARK 3 2 4.8837 - 3.8769 1.00 2737 145 0.1281 0.1746 REMARK 3 3 3.8769 - 3.3870 1.00 2695 158 0.1423 0.1840 REMARK 3 4 3.3870 - 3.0774 1.00 2693 155 0.1570 0.1889 REMARK 3 5 3.0774 - 2.8569 1.00 2696 132 0.1705 0.2286 REMARK 3 6 2.8569 - 2.6884 1.00 2679 143 0.1656 0.2004 REMARK 3 7 2.6884 - 2.5538 1.00 2638 149 0.1643 0.2363 REMARK 3 8 2.5538 - 2.4427 1.00 2674 147 0.1609 0.2305 REMARK 3 9 2.4427 - 2.3486 1.00 2675 125 0.1605 0.2280 REMARK 3 10 2.3486 - 2.2676 1.00 2657 131 0.1610 0.2330 REMARK 3 11 2.2676 - 2.1967 1.00 2661 132 0.1758 0.2676 REMARK 3 12 2.1967 - 2.1339 1.00 2670 130 0.1834 0.2299 REMARK 3 13 2.1339 - 2.0777 1.00 2643 126 0.1907 0.2627 REMARK 3 14 2.0777 - 2.0270 0.99 2657 145 0.1926 0.2355 REMARK 3 15 2.0270 - 1.9809 0.99 2611 150 0.2279 0.2642 REMARK 3 16 1.9809 - 1.9388 0.98 2600 149 0.2465 0.3389 REMARK 3 17 1.9388 - 1.9000 0.89 2333 123 0.2578 0.2823 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 : 0.40 REMARK 3 B_SOL : 46.12 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.31710 REMARK 3 B22 (A**2) : 1.31710 REMARK 3 B33 (A**2) : -2.63430 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 5161 REMARK 3 ANGLE : 1.120 7080 REMARK 3 CHIRALITY : 0.061 762 REMARK 3 PLANARITY : 0.010 818 REMARK 3 DIHEDRAL : 17.636 2040 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): 35.7495 -25.5804 -9.0924 REMARK 3 T TENSOR REMARK 3 T11: 0.1791 T22: 0.1601 REMARK 3 T33: 0.1812 T12: -0.0312 REMARK 3 T13: 0.0089 T23: 0.0139 REMARK 3 L TENSOR REMARK 3 L11: 0.3514 L22: 0.4650 REMARK 3 L33: 0.8356 L12: 0.2176 REMARK 3 L13: -0.0056 L23: -0.0069 REMARK 3 S TENSOR REMARK 3 S11: 0.0083 S12: 0.0025 S13: -0.0396 REMARK 3 S21: -0.0745 S22: 0.0043 S23: -0.0948 REMARK 3 S31: 0.0470 S32: -0.0506 S33: -0.0145 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 628:697) REMARK 3 ORIGIN FOR THE GROUP (A): 9.0381 -11.7539 -3.2040 REMARK 3 T TENSOR REMARK 3 T11: 0.6078 T22: 0.6422 REMARK 3 T33: 0.2710 T12: 0.3617 REMARK 3 T13: 0.0878 T23: 0.0899 REMARK 3 L TENSOR REMARK 3 L11: 1.4708 L22: 1.8538 REMARK 3 L33: 1.9377 L12: -0.6090 REMARK 3 L13: -0.6647 L23: -1.3362 REMARK 3 S TENSOR REMARK 3 S11: -0.2539 S12: -0.3263 S13: 0.0072 REMARK 3 S21: 0.7268 S22: 0.6415 S23: 0.2248 REMARK 3 S31: -0.8886 S32: -0.5873 S33: -0.3490 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 698:832) REMARK 3 ORIGIN FOR THE GROUP (A): 18.6428 -25.7855 -14.8447 REMARK 3 T TENSOR REMARK 3 T11: 0.1673 T22: 0.2725 REMARK 3 T33: 0.1810 T12: -0.0298 REMARK 3 T13: -0.0037 T23: 0.0453 REMARK 3 L TENSOR REMARK 3 L11: 0.1274 L22: 0.6309 REMARK 3 L33: 1.5280 L12: -0.2348 REMARK 3 L13: 0.4047 L23: -0.4793 REMARK 3 S TENSOR REMARK 3 S11: -0.0604 S12: 0.0275 S13: -0.0140 REMARK 3 S21: -0.0960 S22: 0.2018 S23: 0.1538 REMARK 3 S31: -0.0251 S32: -0.4964 S33: -0.1466 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 101:112) REMARK 3 ORIGIN FOR THE GROUP (A): 36.5261 -22.7189 4.2044 REMARK 3 T TENSOR REMARK 3 T11: 0.1162 T22: 0.1942 REMARK 3 T33: 0.2533 T12: -0.0241 REMARK 3 T13: -0.0149 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 0.0399 L22: 2.0293 REMARK 3 L33: 3.0466 L12: 0.0039 REMARK 3 L13: -0.2901 L23: -1.4981 REMARK 3 S TENSOR REMARK 3 S11: -0.0541 S12: -0.0153 S13: -0.0405 REMARK 3 S21: 0.1271 S22: -0.1202 S23: -0.0996 REMARK 3 S31: -0.1757 S32: 0.3460 S33: 0.1459 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN C AND RESID 203:216) REMARK 3 ORIGIN FOR THE GROUP (A): 34.0305 -23.6671 5.5616 REMARK 3 T TENSOR REMARK 3 T11: 0.1646 T22: 0.2452 REMARK 3 T33: 0.1801 T12: 0.0396 REMARK 3 T13: -0.0230 T23: 0.0199 REMARK 3 L TENSOR REMARK 3 L11: 0.2731 L22: 0.7187 REMARK 3 L33: 1.0557 L12: 0.4310 REMARK 3 L13: 0.0310 L23: -0.1770 REMARK 3 S TENSOR REMARK 3 S11: -0.1501 S12: -0.0492 S13: -0.1501 REMARK 3 S21: 0.0076 S22: 0.1806 S23: -0.0866 REMARK 3 S31: -0.0184 S32: -0.1328 S33: -0.0295 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 3OJS 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_1000061204. 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) : 1.0000 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 A 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 : 47553 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.580 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 (%): 43.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M NA CACODYLATE PH 6.5, 0.2M REMARK 280 NH4OAC, 0.01M MG(OAC)2, 26% PEG 8000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 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 30.06567 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 60.13133 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 60.13133 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 30.06567 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 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 C ACT A 840 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 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 O5' - C5' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG B 108 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG C 205 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG C 206 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DC C 207 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG C 208 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC C 210 O4' - C1' - C2' ANGL. DEV. = 3.6 DEGREES REMARK 500 DT C 212 O4' - C1' - N1 ANGL. DEV. = -4.9 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 ARG A 328 141.93 -172.55 REMARK 500 ASP A 381 112.69 -164.31 REMARK 500 THR A 399 -164.45 -105.88 REMARK 500 VAL A 433 -75.92 -120.74 REMARK 500 HIS A 526 135.38 -171.85 REMARK 500 TYR A 545 -57.38 -125.68 REMARK 500 VAL A 586 -15.84 -154.15 REMARK 500 HIS A 784 -58.36 76.86 REMARK 500 TYR A 811 96.18 -160.09 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 835 REMARK 610 PGE A 837 REMARK 610 PGE A 838 REMARK 610 PGE C 6 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 7 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 XJS A 1 O6 REMARK 620 2 XJS A 1 O11 86.4 REMARK 620 3 XJS A 1 O9 91.8 90.5 REMARK 620 4 ASP A 610 OD1 83.2 95.2 172.2 REMARK 620 5 TYR A 611 O 91.5 177.3 91.4 82.7 REMARK 620 6 ASP A 785 OD2 172.9 93.1 95.2 89.8 88.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 8 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 XJS A 1 O11 REMARK 620 2 HOH A 216 O 164.5 REMARK 620 3 ASP A 610 OD2 97.0 97.3 REMARK 620 4 ASP A 785 OD1 86.5 93.6 112.1 REMARK 620 5 HOH A 833 O 84.0 90.3 88.9 157.8 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 XJS A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL 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 MG A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 835 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 836 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 837 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 838 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 840 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 841 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE C 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 9 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KTQ 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 REMARK 900 RELATED ID: 3OJU RELATED DB: PDB DBREF 3OJS A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 3OJS B 101 112 PDB 3OJS 3OJS 101 112 DBREF 3OJS C 201 216 PDB 3OJS 3OJS 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 3OJS DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC B 112 30 HET XJS A 1 69 HET GOL A 2 14 HET GOL A 3 14 HET GOL A 5 14 HET GOL A 4 14 HET GOL A 6 14 HET MG A 7 1 HET MG A 8 1 HET PGE A 835 8 HET ACT A 836 7 HET PGE A 837 8 HET PGE A 838 8 HET ACT A 840 7 HET ACT A 841 7 HET GOL B 7 14 HET PGE C 6 9 HET GOL C 8 14 HET GOL C 9 14 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM XJS 2'-DEOXY-5-[9-(3-{[4-(DIETHYLAMINO)-4- HETNAM 2 XJS OXOBUTANOYL]AMINO}PROPYL)-18-ETHYL-5,8,14,17-TETRAOXO- HETNAM 3 XJS 4,9,13,18-TETRAAZAICOS-1-YN-1-YL]URIDINE 5'- HETNAM 4 XJS (TETRAHYDROGEN TRIPHOSPHATE) HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM PGE TRIETHYLENE GLYCOL HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 XJS C38 H63 N8 O20 P3 FORMUL 5 GOL 8(C3 H8 O3) FORMUL 10 MG 2(MG 2+) FORMUL 12 PGE 4(C6 H14 O4) FORMUL 13 ACT 3(C2 H3 O2 1-) FORMUL 22 HOH *331(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 PHE A 647 1 11 HELIX 17 17 PRO A 650 VAL A 654 5 5 HELIX 18 18 ASP A 655 TYR A 671 1 17 HELIX 19 19 SER A 674 ALA A 683 1 10 HELIX 20 20 PRO A 685 PHE A 700 1 16 HELIX 21 21 PRO A 701 GLY A 718 1 18 HELIX 22 22 PRO A 731 ALA A 735 5 5 HELIX 23 23 VAL A 737 MET A 775 1 39 HELIX 24 24 ARG A 795 GLY A 809 1 15 HELIX 25 25 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 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 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 DOC B 112 1555 1555 1.61 LINK O6 XJS A 1 MG MG A 7 1555 1555 2.09 LINK O11 XJS A 1 MG MG A 7 1555 1555 2.13 LINK O9 XJS A 1 MG MG A 7 1555 1555 2.17 LINK O11 XJS A 1 MG MG A 8 1555 1555 2.33 LINK MG MG A 7 OD1 ASP A 610 1555 1555 2.20 LINK MG MG A 7 O TYR A 611 1555 1555 2.17 LINK MG MG A 7 OD2 ASP A 785 1555 1555 2.13 LINK MG MG A 8 O HOH A 216 1555 1555 2.44 LINK MG MG A 8 OD2 ASP A 610 1555 1555 2.44 LINK MG MG A 8 OD1 ASP A 785 1555 1555 2.30 LINK MG MG A 8 O HOH A 833 1555 1555 2.58 CISPEP 1 TRP A 299 PRO A 300 0 0.64 CISPEP 2 ASP A 578 PRO A 579 0 6.13 SITE 1 AC1 33 MG A 7 MG A 8 HOH A 33 HOH A 115 SITE 2 AC1 33 HOH A 120 HOH A 162 HOH A 185 HOH A 248 SITE 3 AC1 33 ARG A 573 ARG A 587 ASP A 610 TYR A 611 SITE 4 AC1 33 SER A 612 GLN A 613 ILE A 614 GLU A 615 SITE 5 AC1 33 HIS A 639 ARG A 659 ARG A 660 LYS A 663 SITE 6 AC1 33 PHE A 667 ARG A 677 ASP A 785 HOH A 833 SITE 7 AC1 33 HOH B 28 DC B 111 DOC B 112 GOL C 8 SITE 8 AC1 33 HOH C 33 HOH C 42 DA C 204 DG C 205 SITE 9 AC1 33 DG C 206 SITE 1 AC2 10 GOL A 6 HOH A 37 HOH A 55 HOH A 100 SITE 2 AC2 10 ASN A 485 SER A 486 ARG A 487 ASP A 488 SITE 3 AC2 10 DG C 211 DT C 212 SITE 1 AC3 9 HOH A 142 HOH A 219 HOH A 221 HOH A 282 SITE 2 AC3 9 ASP A 452 TYR A 455 ARG A 596 ILE A 599 SITE 3 AC3 9 ASP A 826 SITE 1 AC4 10 HOH A 126 HOH A 168 THR A 544 TYR A 545 SITE 2 AC4 10 PRO A 579 ASN A 580 ASN A 583 PGE C 6 SITE 3 AC4 10 DC C 209 DC C 210 SITE 1 AC5 6 HOH A 53 HOH A 176 ARG A 313 TRP A 318 SITE 2 AC5 6 ASP A 551 LEU A 552 SITE 1 AC6 10 GOL A 2 HOH A 37 HOH A 67 HOH A 125 SITE 2 AC6 10 HOH A 223 ASN A 485 ARG A 487 DG B 107 SITE 3 AC6 10 DG B 108 DC B 109 SITE 1 AC7 5 XJS A 1 MG A 8 ASP A 610 TYR A 611 SITE 2 AC7 5 ASP A 785 SITE 1 AC8 7 XJS A 1 MG A 7 HOH A 216 ASP A 610 SITE 2 AC8 7 ASP A 785 HOH A 833 DOC B 112 SITE 1 AC9 6 HOH A 188 HOH A 198 GLU A 462 GLU A 466 SITE 2 AC9 6 ARG A 593 GLU A 825 SITE 1 BC1 5 HOH A 58 HOH A 183 HOH A 220 ARG A 425 SITE 2 BC1 5 PHE A 724 SITE 1 BC2 5 HOH A 152 GLU A 742 GLU A 745 ARG A 746 SITE 2 BC2 5 DA C 203 SITE 1 BC3 5 HOH A 155 HOH A 166 VAL A 310 LEU A 311 SITE 2 BC3 5 ARG A 405 SITE 1 BC4 3 HOH A 150 HOH A 235 TYR A 455 SITE 1 BC5 3 TRP A 417 ARG A 431 ARG A 435 SITE 1 BC6 12 HOH B 21 HOH B 26 HOH B 27 HOH B 30 SITE 2 BC6 12 DC B 106 DG B 107 DG B 108 DC B 109 SITE 3 BC6 12 HOH C 27 HOH C 37 DG C 208 DC C 209 SITE 1 BC7 5 GOL A 4 HOH A 132 ASP A 578 DC C 209 SITE 2 BC7 5 DC C 210 SITE 1 BC8 4 XJS A 1 HOH C 24 DG C 205 DG C 206 SITE 1 BC9 3 ARG A 728 DG C 206 DC C 207 CRYST1 107.829 107.829 90.197 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 0.009274 0.005354 0.000000 0.00000 SCALE2 0.000000 0.010709 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011087 0.00000