HEADER TRANSFERASE/DNA 23-JAN-12 4DF8 TITLE CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM TITLE 2 THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH AMINOPENTINYL-7- TITLE 3 DEAZA-2-DATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KLENOW FRAGMENT; 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 FRAGMENT: DNA PRIMER; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- COMPND 15 3'); COMPND 16 CHAIN: C; COMPND 17 FRAGMENT: DNA TEMPLATE; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POL I, POL1, POLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET SERIES; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: DNA SYNTHESIZER; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: DNA SYNTHESIZER 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 4DF8 1 REMARK LINK REVDAT 2 08-AUG-12 4DF8 1 JRNL REVDAT 1 16-MAY-12 4DF8 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) : 47.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.260 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 80633 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 4047 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 47.0421 - 6.1403 1.00 2636 154 0.1634 0.1744 REMARK 3 2 6.1403 - 4.8754 1.00 2635 147 0.1772 0.2070 REMARK 3 3 4.8754 - 4.2596 1.00 2679 117 0.1464 0.2323 REMARK 3 4 4.2596 - 3.8703 1.00 2598 172 0.1580 0.1664 REMARK 3 5 3.8703 - 3.5930 1.00 2620 171 0.1615 0.2221 REMARK 3 6 3.5930 - 3.3812 1.00 2624 147 0.1720 0.1925 REMARK 3 7 3.3812 - 3.2119 1.00 2621 140 0.1786 0.2005 REMARK 3 8 3.2119 - 3.0721 1.00 2649 146 0.1888 0.2322 REMARK 3 9 3.0721 - 2.9539 1.00 2674 121 0.2057 0.2990 REMARK 3 10 2.9539 - 2.8520 1.00 2626 155 0.2049 0.2535 REMARK 3 11 2.8520 - 2.7628 1.00 2620 156 0.2096 0.2587 REMARK 3 12 2.7628 - 2.6839 1.00 2686 142 0.2161 0.2541 REMARK 3 13 2.6839 - 2.6132 1.00 2584 136 0.2287 0.3303 REMARK 3 14 2.6132 - 2.5495 1.00 2692 153 0.2108 0.2696 REMARK 3 15 2.5495 - 2.4915 1.00 2611 161 0.2022 0.2443 REMARK 3 16 2.4915 - 2.4385 1.00 2626 130 0.2091 0.2811 REMARK 3 17 2.4385 - 2.3897 1.00 2671 130 0.2131 0.2890 REMARK 3 18 2.3897 - 2.3446 1.00 2676 103 0.2139 0.2769 REMARK 3 19 2.3446 - 2.3027 1.00 2650 123 0.2097 0.2410 REMARK 3 20 2.3027 - 2.2637 1.00 2595 152 0.2212 0.2630 REMARK 3 21 2.2637 - 2.2272 1.00 2706 143 0.2234 0.2690 REMARK 3 22 2.2272 - 2.1929 1.00 2691 101 0.2390 0.2962 REMARK 3 23 2.1929 - 2.1607 1.00 2588 143 0.2431 0.3025 REMARK 3 24 2.1607 - 2.1302 1.00 2664 128 0.2484 0.2851 REMARK 3 25 2.1302 - 2.1015 1.00 2666 126 0.2598 0.2672 REMARK 3 26 2.1015 - 2.0742 1.00 2690 137 0.2748 0.2829 REMARK 3 27 2.0742 - 2.0482 1.00 2523 136 0.2913 0.3555 REMARK 3 28 2.0482 - 2.0236 1.00 2707 127 0.3303 0.3011 REMARK 3 29 2.0236 - 2.0000 0.97 2578 150 0.3674 0.4256 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.06 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 30.93 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.00890 REMARK 3 B22 (A**2) : 8.00890 REMARK 3 B33 (A**2) : -6.52380 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 : 0.014 5093 REMARK 3 ANGLE : 0.993 7019 REMARK 3 CHIRALITY : 0.050 765 REMARK 3 PLANARITY : 0.004 807 REMARK 3 DIHEDRAL : 17.532 1963 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): 40.0521 -43.0445 -17.7416 REMARK 3 T TENSOR REMARK 3 T11: 0.1903 T22: 0.1476 REMARK 3 T33: 0.2309 T12: -0.0313 REMARK 3 T13: 0.0434 T23: -0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.1542 L22: 0.3379 REMARK 3 L33: 0.2096 L12: -0.1027 REMARK 3 L13: 0.0432 L23: 0.1875 REMARK 3 S TENSOR REMARK 3 S11: -0.0287 S12: -0.0452 S13: -0.1595 REMARK 3 S21: -0.1325 S22: 0.0154 S23: -0.0992 REMARK 3 S31: 0.1594 S32: 0.0553 S33: -0.0010 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 434:603) REMARK 3 ORIGIN FOR THE GROUP (A): 35.8451 -12.5349 -0.7127 REMARK 3 T TENSOR REMARK 3 T11: 0.1906 T22: 0.1328 REMARK 3 T33: 0.1545 T12: -0.0336 REMARK 3 T13: 0.0265 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 0.3881 L22: 0.5216 REMARK 3 L33: 0.3068 L12: 0.4277 REMARK 3 L13: 0.0991 L23: -0.0615 REMARK 3 S TENSOR REMARK 3 S11: 0.0161 S12: -0.0530 S13: 0.0200 REMARK 3 S21: 0.0152 S22: -0.0312 S23: 0.0308 REMARK 3 S31: -0.1708 S32: -0.0045 S33: -0.0294 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 604:685) REMARK 3 ORIGIN FOR THE GROUP (A): 11.4949 -14.0035 -8.5233 REMARK 3 T TENSOR REMARK 3 T11: 0.2200 T22: 0.4015 REMARK 3 T33: 0.1367 T12: 0.2691 REMARK 3 T13: -0.0520 T23: 0.0358 REMARK 3 L TENSOR REMARK 3 L11: 0.2894 L22: 0.5746 REMARK 3 L33: 0.4609 L12: 0.1234 REMARK 3 L13: 0.1227 L23: -0.0058 REMARK 3 S TENSOR REMARK 3 S11: -0.3899 S12: -0.0957 S13: 0.0014 REMARK 3 S21: -0.0145 S22: 0.3121 S23: 0.0018 REMARK 3 S31: -0.5280 S32: -0.6416 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 686:832) REMARK 3 ORIGIN FOR THE GROUP (A): 17.2552 -25.0954 -13.1788 REMARK 3 T TENSOR REMARK 3 T11: 0.0722 T22: 0.2820 REMARK 3 T33: 0.1288 T12: -0.0164 REMARK 3 T13: 0.0095 T23: 0.0598 REMARK 3 L TENSOR REMARK 3 L11: 0.2781 L22: 0.5601 REMARK 3 L33: 0.8623 L12: -0.0728 REMARK 3 L13: 0.3006 L23: 0.0358 REMARK 3 S TENSOR REMARK 3 S11: -0.1220 S12: -0.0669 S13: -0.0875 REMARK 3 S21: -0.0893 S22: 0.0827 S23: 0.0135 REMARK 3 S31: -0.3256 S32: -0.5119 S33: -0.2523 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 4DF8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8 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) : 1.23000 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4300 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 (%) : 99.4 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 : 1.780 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 (%): 44.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 200MM MG-FORMATE, 100 REMARK 280 MMTRIS 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 30.17200 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 60.34400 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 60.34400 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 30.17200 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: 8180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 GLU A 832 CG CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 346 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: 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. = 4.6 DEGREES REMARK 500 DC B 103 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC B 104 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA C 203 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 3.9 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 381 110.13 -166.73 REMARK 500 VAL A 433 -71.33 -123.79 REMARK 500 HIS A 480 149.22 -175.42 REMARK 500 TYR A 545 -58.60 -121.03 REMARK 500 VAL A 586 -17.29 -158.36 REMARK 500 HIS A 784 -68.24 74.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 ASP A 610 OD1 47.9 REMARK 620 3 ASP A 785 OD1 120.2 80.6 REMARK 620 4 0L4 A 901 O2A 101.1 70.9 84.4 REMARK 620 5 HOH A1002 O 100.5 135.7 97.9 153.4 REMARK 620 6 HOH A1019 O 82.4 108.8 152.2 74.8 93.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 903 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 83.9 REMARK 620 3 ASP A 785 OD2 103.8 90.5 REMARK 620 4 0L4 A 901 O2A 98.0 155.6 112.4 REMARK 620 5 0L4 A 901 O2B 157.0 88.2 97.8 80.7 REMARK 620 6 0L4 A 901 O2G 86.6 76.5 162.5 79.3 70.5 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 301 O REMARK 620 2 HOH B 302 O 179.7 REMARK 620 3 HOH B 303 O 89.9 89.8 REMARK 620 4 HOH B 304 O 89.8 90.3 90.3 REMARK 620 5 HOH B 305 O 89.9 90.0 89.8 179.7 REMARK 620 6 HOH C 401 O 90.3 90.1 179.9 89.7 90.1 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 0L4 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL 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 FMT 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 CL A 910 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 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 4DF8 A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4DF8 B 101 112 PDB 4DF8 4DF8 101 112 DBREF 4DF8 C 201 216 PDB 4DF8 4DF8 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 DT DG DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC MODRES 4DF8 DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC B 112 18 HET 0L4 A 901 36 HET MG A 902 1 HET MG A 903 1 HET EDO A 904 4 HET FMT A 905 3 HET CL A 906 1 HET EDO A 907 4 HET FMT A 908 3 HET EDO A 909 4 HET CL A 910 1 HET MG B 201 1 HET EDO C 301 4 HET FMT C 302 3 HET FMT C 303 3 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM 0L4 5-(5-AMINOPENT-1-YN-1-YL)-7-{2-DEOXY-5-O-[(S)- HETNAM 2 0L4 HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 3 0L4 PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO- HETNAM 4 0L4 PENTOFURANOSYL}-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM FMT FORMIC ACID HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 0L4 C16 H24 N5 O12 P3 FORMUL 5 MG 3(MG 2+) FORMUL 7 EDO 4(C2 H6 O2) FORMUL 8 FMT 4(C H2 O2) FORMUL 9 CL 2(CL 1-) FORMUL 18 HOH *203(H2 O) HELIX 1 1 GLU A 337 LEU A 342 1 6 HELIX 2 2 ARG A 343 LEU A 345 5 3 HELIX 3 3 LEU A 352 GLU A 363 1 12 HELIX 4 4 ASP A 372 ASP A 381 1 10 HELIX 5 5 THR A 386 GLY A 395 1 10 HELIX 6 6 GLU A 401 LEU A 420 1 20 HELIX 7 7 GLU A 423 VAL A 433 1 11 HELIX 8 8 VAL A 433 GLY A 448 1 16 HELIX 9 9 ASP A 452 GLY A 479 1 28 HELIX 10 10 SER A 486 ASP A 496 1 11 HELIX 11 11 SER A 515 LEU A 522 1 8 HELIX 12 12 PRO A 527 TYR A 545 1 19 HELIX 13 13 PRO A 548 ILE A 553 5 6 HELIX 14 14 THR A 588 ARG A 596 1 9 HELIX 15 15 GLN A 613 GLY A 624 1 12 HELIX 16 16 ASP A 625 GLU A 634 1 10 HELIX 17 17 ASP A 637 GLY A 648 1 12 HELIX 18 18 PRO A 650 VAL A 654 5 5 HELIX 19 19 ASP A 655 TYR A 671 1 17 HELIX 20 20 SER A 674 ALA A 683 1 10 HELIX 21 21 PRO A 685 SER A 699 1 15 HELIX 22 22 PHE A 700 GLY A 718 1 19 HELIX 23 23 PRO A 731 ALA A 735 5 5 HELIX 24 24 VAL A 737 GLY A 776 1 40 HELIX 25 25 LYS A 793 GLY A 809 1 17 HELIX 26 26 ASP A 826 GLU A 832 1 7 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 GLU A 295 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 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 OD2 ASP A 610 MG MG A 902 1555 1555 2.28 LINK OD1 ASP A 610 MG MG A 902 1555 1555 2.91 LINK OD1 ASP A 610 MG MG A 903 1555 1555 2.09 LINK O TYR A 611 MG MG A 903 1555 1555 2.17 LINK OD1 ASP A 785 MG MG A 902 1555 1555 2.28 LINK OD2 ASP A 785 MG MG A 903 1555 1555 1.92 LINK O2A 0L4 A 901 MG MG A 902 1555 1555 2.48 LINK O2A 0L4 A 901 MG MG A 903 1555 1555 2.08 LINK O2B 0L4 A 901 MG MG A 903 1555 1555 2.10 LINK O2G 0L4 A 901 MG MG A 903 1555 1555 2.17 LINK MG MG A 902 O HOH A1002 1555 1555 2.51 LINK MG MG A 902 O HOH A1019 1555 1555 2.74 LINK MG MG B 201 O HOH B 301 1555 1555 2.18 LINK MG MG B 201 O HOH B 302 1555 1555 2.18 LINK MG MG B 201 O HOH B 303 1555 1555 2.18 LINK MG MG B 201 O HOH B 304 1555 1555 2.18 LINK MG MG B 201 O HOH B 305 1555 1555 2.18 LINK MG MG B 201 O HOH C 401 1555 1555 2.18 CISPEP 1 TRP A 299 PRO A 300 0 2.91 CISPEP 2 ASP A 578 PRO A 579 0 0.73 SITE 1 AC1 25 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC1 25 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC1 25 ARG A 659 ARG A 660 LYS A 663 PHE A 667 SITE 4 AC1 25 ASP A 785 MG A 902 MG A 903 EDO A 907 SITE 5 AC1 25 CL A 910 HOH A1001 HOH A1007 HOH A1019 SITE 6 AC1 25 HOH A1049 HOH A1106 DOC B 112 DT C 204 SITE 7 AC1 25 DG C 205 SITE 1 AC2 6 ASP A 610 ASP A 785 0L4 A 901 MG A 903 SITE 2 AC2 6 HOH A1002 HOH A1019 SITE 1 AC3 5 ASP A 610 TYR A 611 ASP A 785 0L4 A 901 SITE 2 AC3 5 MG A 902 SITE 1 AC4 4 LYS A 354 ASP A 355 GLN A 566 HOH A1010 SITE 1 AC5 3 LEU A 311 ARG A 405 HOH A1096 SITE 1 AC6 1 ARG A 313 SITE 1 AC7 8 ARG A 573 GLU A 615 GLN A 754 ALA A 757 SITE 2 AC7 8 ALA A 758 HIS A 784 0L4 A 901 HOH A1079 SITE 1 AC8 1 ARG A 704 SITE 1 AC9 6 ASP A 488 LYS A 511 DC B 106 DG B 107 SITE 2 AC9 6 DG C 211 DT C 212 SITE 1 BC1 3 ARG A 660 LYS A 663 0L4 A 901 SITE 1 BC2 6 HOH B 301 HOH B 302 HOH B 303 HOH B 304 SITE 2 BC2 6 HOH B 305 HOH C 401 SITE 1 BC3 2 DG C 206 FMT C 302 SITE 1 BC4 2 DG C 205 EDO C 301 SITE 1 BC5 3 ARG A 728 DG C 206 DC C 207 CRYST1 108.609 108.609 90.516 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 0.009207 0.005316 0.000000 0.00000 SCALE2 0.000000 0.010632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011048 0.00000