HEADER TRANSFERASE/DNA 24-JAN-12 4DFP TITLE CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM TITLE 2 THERMUS AQAUTICUS IN A TERNARY COMPLEX WITH 7-(AMINOPENTINYL)-7- TITLE 3 DEAZA-DGTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KLENOW FRAGMENT, UNP RESIDUES 293-831; 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 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(AAACGGCGCCGTGGTC)-3'; COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES 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: PET21B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS DNA POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.BERGEN,A.STECK,S.STRUETT,A.BACCARO,W.WELTE,K.DIEDERICHS,A.MARX REVDAT 3 13-SEP-23 4DFP 1 REMARK LINK REVDAT 2 08-AUG-12 4DFP 1 JRNL REVDAT 1 16-MAY-12 4DFP 0 JRNL AUTH K.BERGEN,A.L.STECK,S.STRUTT,A.BACCARO,W.WELTE,K.DIEDERICHS, JRNL AUTH 2 A.MARX JRNL TITL STRUCTURES OF KLENTAQ DNA POLYMERASE CAUGHT WHILE JRNL TITL 2 INCORPORATING C5-MODIFIED PYRIMIDINE AND C7-MODIFIED JRNL TITL 3 7-DEAZAPURINE NUCLEOSIDE TRIPHOSPHATES. JRNL REF J.AM.CHEM.SOC. V. 134 11840 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 22475415 JRNL DOI 10.1021/JA3017889 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 41788 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2077 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 46.9723 - 4.9308 1.00 2786 161 0.1862 0.2033 REMARK 3 2 4.9308 - 3.9143 1.00 2691 139 0.1499 0.1637 REMARK 3 3 3.9143 - 3.4197 1.00 2675 156 0.1556 0.2002 REMARK 3 4 3.4197 - 3.1071 1.00 2645 149 0.1792 0.2172 REMARK 3 5 3.1071 - 2.8844 1.00 2654 133 0.1968 0.2494 REMARK 3 6 2.8844 - 2.7144 1.00 2627 142 0.2090 0.2430 REMARK 3 7 2.7144 - 2.5785 1.00 2639 150 0.2022 0.2973 REMARK 3 8 2.5785 - 2.4662 1.00 2630 148 0.2002 0.2400 REMARK 3 9 2.4662 - 2.3713 1.00 2628 121 0.1971 0.2668 REMARK 3 10 2.3713 - 2.2895 1.00 2663 124 0.1959 0.2616 REMARK 3 11 2.2895 - 2.2179 1.00 2601 139 0.1992 0.2519 REMARK 3 12 2.2179 - 2.1545 1.00 2660 125 0.2072 0.2847 REMARK 3 13 2.1545 - 2.0978 1.00 2622 125 0.2288 0.2505 REMARK 3 14 2.0978 - 2.0466 1.00 2598 131 0.2484 0.3233 REMARK 3 15 2.0466 - 2.0001 0.98 2592 134 0.2773 0.3193 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.40 REMARK 3 SHRINKAGE RADIUS : 1.24 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 38.30 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.90330 REMARK 3 B22 (A**2) : 1.90330 REMARK 3 B33 (A**2) : -3.24580 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 : 0.009 5113 REMARK 3 ANGLE : 0.836 7052 REMARK 3 CHIRALITY : 0.048 768 REMARK 3 PLANARITY : 0.003 808 REMARK 3 DIHEDRAL : 15.745 1962 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 294:433) REMARK 3 ORIGIN FOR THE GROUP (A): 39.7928 -43.2687 -17.6018 REMARK 3 T TENSOR REMARK 3 T11: 0.2381 T22: 0.2092 REMARK 3 T33: 0.2477 T12: -0.0213 REMARK 3 T13: 0.0343 T23: 0.0120 REMARK 3 L TENSOR REMARK 3 L11: 0.4267 L22: 0.9174 REMARK 3 L33: 0.3113 L12: -0.4852 REMARK 3 L13: 0.0031 L23: 0.2904 REMARK 3 S TENSOR REMARK 3 S11: -0.0753 S12: -0.0074 S13: -0.1031 REMARK 3 S21: -0.1040 S22: 0.0328 S23: -0.1083 REMARK 3 S31: 0.1550 S32: 0.0519 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 434:603) REMARK 3 ORIGIN FOR THE GROUP (A): 35.8630 -12.5088 -0.7169 REMARK 3 T TENSOR REMARK 3 T11: 0.2159 T22: 0.1918 REMARK 3 T33: 0.2086 T12: -0.0061 REMARK 3 T13: 0.0012 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.4434 L22: 0.6334 REMARK 3 L33: 0.5764 L12: 0.4724 REMARK 3 L13: 0.0455 L23: 0.1464 REMARK 3 S TENSOR REMARK 3 S11: 0.0049 S12: -0.0533 S13: 0.0170 REMARK 3 S21: -0.0316 S22: -0.0240 S23: 0.0528 REMARK 3 S31: -0.1324 S32: -0.0203 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 604:685) REMARK 3 ORIGIN FOR THE GROUP (A): 11.5947 -13.8497 -8.5376 REMARK 3 T TENSOR REMARK 3 T11: 0.3529 T22: 0.4328 REMARK 3 T33: 0.2024 T12: 0.1645 REMARK 3 T13: -0.0177 T23: -0.0197 REMARK 3 L TENSOR REMARK 3 L11: 0.5265 L22: 0.5037 REMARK 3 L33: 0.4976 L12: -0.1786 REMARK 3 L13: 0.5426 L23: -0.3637 REMARK 3 S TENSOR REMARK 3 S11: -0.1405 S12: -0.2479 S13: 0.1441 REMARK 3 S21: 0.1977 S22: 0.2156 S23: -0.0340 REMARK 3 S31: -0.5985 S32: -0.5183 S33: 0.0527 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 686:832) REMARK 3 ORIGIN FOR THE GROUP (A): 17.2609 -24.9232 -13.0888 REMARK 3 T TENSOR REMARK 3 T11: 0.1694 T22: 0.2685 REMARK 3 T33: 0.1764 T12: 0.0322 REMARK 3 T13: -0.0027 T23: 0.0343 REMARK 3 L TENSOR REMARK 3 L11: 0.3588 L22: 0.5968 REMARK 3 L33: 1.8608 L12: 0.0562 REMARK 3 L13: 0.1552 L23: -0.3276 REMARK 3 S TENSOR REMARK 3 S11: -0.1140 S12: 0.0123 S13: -0.0725 REMARK 3 S21: -0.0471 S22: 0.1379 S23: 0.0595 REMARK 3 S31: -0.1908 S32: -0.5015 S33: -0.2028 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 4DFP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000070271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : 0.900000 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT, SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL 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 : 41791 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 46.959 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.690 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIFFERENCE FOURIER REMARK 200 TECHNIQUES REMARK 200 SOFTWARE USED: PHENIX 1.7.3_928 REMARK 200 STARTING MODEL: PDB ENTRY 3M8S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 200MM MG-FORMATE, 100 MM REMARK 280 TRIS PH 8.0 , VAPOR DIFFUSION, HANGING 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 30.14500 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 60.29000 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 60.29000 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 30.14500 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: 8790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 GLU A 462 CG CD OE1 OE2 REMARK 470 GLU A 530 CG CD OE1 OE2 REMARK 470 PHE A 647 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 832 CG CD OE1 OE2 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. = 3.2 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DOC B 112 O3' - P - OP2 ANGL. DEV. = 8.0 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 2.7 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 381 111.52 -160.75 REMARK 500 THR A 399 -167.05 -109.51 REMARK 500 VAL A 433 -71.40 -121.12 REMARK 500 HIS A 480 148.11 -170.02 REMARK 500 TYR A 545 -59.26 -120.76 REMARK 500 VAL A 586 -14.47 -161.22 REMARK 500 HIS A 784 -66.61 71.06 REMARK 500 TYR A 811 89.32 -163.34 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 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 87.2 REMARK 620 3 ASP A 785 OD1 107.8 103.5 REMARK 620 4 0L7 A 908 O2A 99.3 150.8 101.5 REMARK 620 5 0L7 A 908 O1B 154.6 93.7 96.7 68.4 REMARK 620 6 0L7 A 908 O1G 88.6 79.8 163.3 72.0 66.7 REMARK 620 N 1 2 3 4 5 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 OD2 REMARK 620 2 ASP A 785 OD2 120.5 REMARK 620 3 0L7 A 908 O2A 90.4 86.0 REMARK 620 4 HOH A1001 O 101.3 102.9 158.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 910 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1204 O REMARK 620 2 HOH A1205 O 179.8 REMARK 620 3 HOH A1206 O 90.0 90.2 REMARK 620 4 HOH A1207 O 89.9 90.2 89.8 REMARK 620 5 HOH B 327 O 90.2 89.7 179.8 90.1 REMARK 620 6 HOH C 432 O 89.9 90.1 90.0 179.7 90.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 913 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1210 O REMARK 620 2 HOH A1211 O 179.1 REMARK 620 3 HOH A1212 O 90.6 88.5 REMARK 620 4 HOH A1213 O 89.9 90.1 90.2 REMARK 620 5 HOH A1214 O 90.2 89.8 89.5 179.6 REMARK 620 6 HOH A1215 O 90.2 90.7 179.2 90.0 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 322 O REMARK 620 2 HOH B 323 O 179.8 REMARK 620 3 HOH B 324 O 90.1 90.0 REMARK 620 4 HOH B 325 O 89.7 90.1 90.0 REMARK 620 5 HOH B 326 O 90.1 89.9 179.8 90.1 REMARK 620 6 HOH C 431 O 90.1 90.1 90.0 179.8 89.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG 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 EDO A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0L7 A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 909 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 910 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 911 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 912 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 913 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT C 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KTQ RELATED DB: PDB REMARK 900 RELATED ID: 3OJU RELATED DB: PDB REMARK 900 RELATED ID: 3OJS RELATED DB: PDB REMARK 900 RELATED ID: 3LWM RELATED DB: PDB REMARK 900 RELATED ID: 3LWL RELATED DB: PDB REMARK 900 RELATED ID: 3M8S RELATED DB: PDB DBREF 4DFP A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4DFP B 101 112 PDB 4DFP 4DFP 101 112 DBREF 4DFP C 201 216 PDB 4DFP 4DFP 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 DC DG DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC MODRES 4DFP DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC B 112 18 HET MG A 901 1 HET MG A 902 1 HET EDO A 903 4 HET FMT A 904 3 HET EDO A 905 4 HET FMT A 906 3 HET FMT A 907 3 HET 0L7 A 908 37 HET EDO A 909 4 HET MG A 910 1 HET EDO A 911 4 HET FMT A 912 3 HET MG A 913 1 HET FMT B 201 3 HET MG B 202 1 HET FMT C 301 3 HET EDO C 302 4 HET FMT C 303 3 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM FMT FORMIC ACID HETNAM 0L7 2-AMINO-5-(5-AMINOPENT-1-YN-1-YL)-7-{2-DEOXY-5-O-[(S)- HETNAM 2 0L7 HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 3 0L7 PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO- HETNAM 4 0L7 PENTOFURANOSYL}-3,7-DIHYDRO-4H-PYRROLO[2,3- HETNAM 5 0L7 D]PYRIMIDIN-4-ONE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 MG 5(MG 2+) FORMUL 6 EDO 5(C2 H6 O2) FORMUL 7 FMT 7(C H2 O2) FORMUL 11 0L7 C16 H24 N5 O13 P3 FORMUL 22 HOH *278(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 PHE A 647 1 11 HELIX 18 18 ASP A 655 TYR A 671 1 17 HELIX 19 19 SER A 674 LEU A 682 1 9 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 GLY A 776 1 40 HELIX 24 24 ARG A 795 GLY A 809 1 15 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 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 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 1.60 LINK OD1 ASP A 610 MG MG A 901 1555 1555 2.11 LINK OD2 ASP A 610 MG MG A 902 1555 1555 2.93 LINK O TYR A 611 MG MG A 901 1555 1555 2.14 LINK OD1 ASP A 785 MG MG A 901 1555 1555 2.00 LINK OD2 ASP A 785 MG MG A 902 1555 1555 2.16 LINK MG MG A 901 O2A 0L7 A 908 1555 1555 2.20 LINK MG MG A 901 O1B 0L7 A 908 1555 1555 2.21 LINK MG MG A 901 O1G 0L7 A 908 1555 1555 2.32 LINK MG MG A 902 O2A 0L7 A 908 1555 1555 2.62 LINK MG MG A 902 O HOH A1001 1555 1555 2.04 LINK MG MG A 910 O HOH A1204 1555 1555 2.18 LINK MG MG A 910 O HOH A1205 1555 1555 2.18 LINK MG MG A 910 O HOH A1206 1555 1555 2.18 LINK MG MG A 910 O HOH A1207 1555 1555 2.18 LINK MG MG A 910 O HOH B 327 1555 1555 2.18 LINK MG MG A 910 O HOH C 432 1555 1555 2.18 LINK MG MG A 913 O HOH A1210 1555 1555 2.18 LINK MG MG A 913 O HOH A1211 1555 1555 2.18 LINK MG MG A 913 O HOH A1212 1555 1555 2.17 LINK MG MG A 913 O HOH A1213 1555 1555 2.18 LINK MG MG A 913 O HOH A1214 1555 1555 2.18 LINK MG MG A 913 O HOH A1215 1555 1555 2.18 LINK MG MG B 202 O HOH B 322 1555 1555 2.18 LINK MG MG B 202 O HOH B 323 1555 1555 2.18 LINK MG MG B 202 O HOH B 324 1555 1555 2.18 LINK MG MG B 202 O HOH B 325 1555 1555 2.18 LINK MG MG B 202 O HOH B 326 1555 1555 2.18 LINK MG MG B 202 O HOH C 431 1555 1555 2.18 CISPEP 1 TRP A 299 PRO A 300 0 3.19 CISPEP 2 ASP A 578 PRO A 579 0 -1.35 SITE 1 AC1 5 ASP A 610 TYR A 611 ASP A 785 MG A 902 SITE 2 AC1 5 0L7 A 908 SITE 1 AC2 6 ASP A 610 ASP A 785 MG A 901 0L7 A 908 SITE 2 AC2 6 HOH A1001 DOC B 112 SITE 1 AC3 7 ARG A 573 GLU A 615 GLN A 754 ALA A 757 SITE 2 AC3 7 HIS A 784 0L7 A 908 HOH A1060 SITE 1 AC4 3 ARG A 469 GLN A 534 GLU A 794 SITE 1 AC5 4 LYS A 354 ASP A 355 HOH A1012 HOH A1014 SITE 1 AC6 2 HIS A 443 HOH A1117 SITE 1 AC7 5 GLU A 337 PRO A 338 TYR A 339 LYS A 340 SITE 2 AC7 5 DG B 101 SITE 1 AC8 26 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC8 26 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC8 26 ARG A 659 ARG A 660 LYS A 663 THR A 664 SITE 4 AC8 26 PHE A 667 TYR A 671 ASP A 785 MG A 901 SITE 5 AC8 26 MG A 902 EDO A 903 HOH A1031 HOH A1047 SITE 6 AC8 26 HOH A1057 HOH A1072 DOC B 112 HOH B 304 SITE 7 AC8 26 DC C 204 DG C 205 SITE 1 AC9 5 ARG A 801 GLU A 805 LEU A 813 ALA A 814 SITE 2 AC9 5 HOH A1119 SITE 1 BC1 6 HOH A1204 HOH A1205 HOH A1206 HOH A1207 SITE 2 BC1 6 HOH B 327 HOH C 432 SITE 1 BC2 5 ALA A 517 GLU A 520 GLN A 680 DA C 201 SITE 2 BC2 5 DA C 202 SITE 1 BC3 3 ALA A 608 GLU A 820 LYS A 831 SITE 1 BC4 7 GLU A 825 HOH A1210 HOH A1211 HOH A1212 SITE 2 BC4 7 HOH A1213 HOH A1214 HOH A1215 SITE 1 BC5 4 DG B 110 HOH B 307 HOH B 312 HOH B 321 SITE 1 BC6 6 HOH B 322 HOH B 323 HOH B 324 HOH B 325 SITE 2 BC6 6 HOH B 326 HOH C 431 SITE 1 BC7 5 DC C 204 DG C 205 DG C 206 EDO C 302 SITE 2 BC7 5 HOH C 411 SITE 1 BC8 3 DG C 205 DG C 206 FMT C 301 SITE 1 BC9 4 ASP A 578 PRO A 579 DC C 209 HOH C 433 CRYST1 108.448 108.448 90.435 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 0.009221 0.005324 0.000000 0.00000 SCALE2 0.000000 0.010648 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011058 0.00000