HEADER TRANSFERASE/DNA 12-JUL-11 3SV4 TITLE CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM TITLE 2 THERMUS AQUATICUS IN AN OPEN BINARY COMPLEX WITH DT AS TEMPLATING TITLE 3 NUCLEOBASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KLENOW 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: (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(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-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: 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-21B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: DNA SYNTHESIZER; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: DNA SYNTHESIZER KEYWDS DNA POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.BETZ,K.DIEDERICHS,A.MARX REVDAT 4 13-SEP-23 3SV4 1 REMARK LINK REVDAT 3 12-SEP-12 3SV4 1 JRNL REVDAT 2 04-JUL-12 3SV4 1 JRNL REVDAT 1 06-JUN-12 3SV4 0 JRNL AUTH K.BETZ,D.A.MALYSHEV,T.LAVERGNE,W.WELTE,K.DIEDERICHS, JRNL AUTH 2 T.J.DWYER,P.ORDOUKHANIAN,F.E.ROMESBERG,A.MARX JRNL TITL KLENTAQ POLYMERASE REPLICATES UNNATURAL BASE PAIRS BY JRNL TITL 2 INDUCING A WATSON-CRICK GEOMETRY. JRNL REF NAT.CHEM.BIOL. V. 8 612 2012 JRNL REFN ISSN 1552-4450 JRNL PMID 22660438 JRNL DOI 10.1038/NCHEMBIO.966 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.300 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 80646 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 4049 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 46.9464 - 6.1233 1.00 2654 154 0.1885 0.2167 REMARK 3 2 6.1233 - 4.8619 1.00 2637 147 0.1768 0.2164 REMARK 3 3 4.8619 - 4.2478 1.00 2689 121 0.1358 0.1948 REMARK 3 4 4.2478 - 3.8596 1.00 2602 168 0.1435 0.1753 REMARK 3 5 3.8596 - 3.5831 1.00 2642 171 0.1544 0.1839 REMARK 3 6 3.5831 - 3.3719 1.00 2622 151 0.1629 0.1983 REMARK 3 7 3.3719 - 3.2031 1.00 2667 138 0.1603 0.1631 REMARK 3 8 3.2031 - 3.0637 1.00 2637 148 0.1722 0.2022 REMARK 3 9 3.0637 - 2.9457 1.00 2667 127 0.1689 0.2243 REMARK 3 10 2.9457 - 2.8441 1.00 2659 153 0.1748 0.2104 REMARK 3 11 2.8441 - 2.7552 1.00 2632 155 0.1812 0.2302 REMARK 3 12 2.7552 - 2.6764 1.00 2643 137 0.1861 0.2403 REMARK 3 13 2.6764 - 2.6060 1.00 2631 141 0.1882 0.2025 REMARK 3 14 2.6060 - 2.5424 1.00 2691 151 0.1827 0.2467 REMARK 3 15 2.5424 - 2.4846 1.00 2612 156 0.1875 0.2639 REMARK 3 16 2.4846 - 2.4317 1.00 2661 138 0.1963 0.2458 REMARK 3 17 2.4317 - 2.3831 1.00 2708 125 0.2025 0.2676 REMARK 3 18 2.3831 - 2.3381 1.00 2638 113 0.1995 0.2498 REMARK 3 19 2.3381 - 2.2964 1.00 2663 130 0.1971 0.2565 REMARK 3 20 2.2964 - 2.2574 1.00 2633 140 0.1906 0.2171 REMARK 3 21 2.2574 - 2.2210 1.00 2704 145 0.1985 0.2257 REMARK 3 22 2.2210 - 2.1869 1.00 2672 106 0.2090 0.2585 REMARK 3 23 2.1869 - 2.1547 1.00 2629 134 0.2183 0.2772 REMARK 3 24 2.1547 - 2.1244 1.00 2686 134 0.2217 0.2730 REMARK 3 25 2.1244 - 2.0956 1.00 2681 127 0.2313 0.2683 REMARK 3 26 2.0956 - 2.0684 1.00 2609 136 0.2401 0.2608 REMARK 3 27 2.0684 - 2.0426 1.00 2634 148 0.2428 0.2993 REMARK 3 28 2.0426 - 2.0180 1.00 2673 130 0.2765 0.2401 REMARK 3 29 2.0180 - 1.9945 0.87 2321 125 0.3185 0.3798 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.89 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 44.15 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.560 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.710 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) : 1.13150 REMARK 3 B22 (A**2) : 1.13150 REMARK 3 B33 (A**2) : -2.26300 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 : 0.003 5040 REMARK 3 ANGLE : 0.770 6952 REMARK 3 CHIRALITY : 0.043 761 REMARK 3 PLANARITY : 0.003 812 REMARK 3 DIHEDRAL : 15.874 1960 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 293:603) REMARK 3 ORIGIN FOR THE GROUP (A): 37.6550 -26.3387 -8.5647 REMARK 3 T TENSOR REMARK 3 T11: 0.1277 T22: 0.2203 REMARK 3 T33: 0.1580 T12: -0.0279 REMARK 3 T13: 0.0072 T23: 0.0260 REMARK 3 L TENSOR REMARK 3 L11: 0.5248 L22: 1.9081 REMARK 3 L33: 1.0648 L12: 0.4288 REMARK 3 L13: 0.1842 L23: 0.4177 REMARK 3 S TENSOR REMARK 3 S11: 0.0357 S12: -0.0715 S13: -0.0192 REMARK 3 S21: 0.1109 S22: -0.0065 S23: -0.0798 REMARK 3 S31: 0.0072 S32: 0.0794 S33: -0.0327 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 604:832) REMARK 3 ORIGIN FOR THE GROUP (A): 14.5802 -22.2552 -11.7121 REMARK 3 T TENSOR REMARK 3 T11: 0.2438 T22: 0.3409 REMARK 3 T33: 0.2178 T12: 0.0515 REMARK 3 T13: 0.0671 T23: 0.0170 REMARK 3 L TENSOR REMARK 3 L11: 1.9534 L22: 1.6041 REMARK 3 L33: 2.4788 L12: 0.6463 REMARK 3 L13: -0.0556 L23: -1.1350 REMARK 3 S TENSOR REMARK 3 S11: 0.0919 S12: -0.2987 S13: 0.2273 REMARK 3 S21: 0.2721 S22: 0.1545 S23: 0.3641 REMARK 3 S31: -0.4667 S32: -0.5358 S33: -0.1619 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' REMARK 3 ORIGIN FOR THE GROUP (A): 36.5555 -22.7340 4.3165 REMARK 3 T TENSOR REMARK 3 T11: 0.2754 T22: 0.3418 REMARK 3 T33: 0.2524 T12: 0.0635 REMARK 3 T13: -0.0113 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 4.5008 L22: 1.5141 REMARK 3 L33: 0.5138 L12: 1.3478 REMARK 3 L13: -0.4867 L23: -0.6079 REMARK 3 S TENSOR REMARK 3 S11: 0.1457 S12: 0.1921 S13: -0.6158 REMARK 3 S21: 0.3825 S22: -0.3798 S23: -0.0349 REMARK 3 S31: -0.0933 S32: 0.6923 S33: 0.1890 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' REMARK 3 ORIGIN FOR THE GROUP (A): 33.4745 -22.6881 4.0917 REMARK 3 T TENSOR REMARK 3 T11: 0.2444 T22: 0.2387 REMARK 3 T33: 0.1312 T12: 0.0531 REMARK 3 T13: -0.0113 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 1.6568 L22: 3.7073 REMARK 3 L33: 3.0019 L12: 1.5370 REMARK 3 L13: -1.2632 L23: 0.9220 REMARK 3 S TENSOR REMARK 3 S11: -0.3296 S12: 0.1692 S13: 0.0002 REMARK 3 S21: 0.2317 S22: 0.2817 S23: 0.0680 REMARK 3 S31: -0.0944 S32: 0.0803 S33: 0.1012 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 3SV4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000066689. 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 : 8.5 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) : 0.9000 REMARK 200 MONOCHROMATOR : NULL 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 : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 47.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.980 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 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 : 2.060 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHENIX 1.7.1_743 REMARK 200 STARTING MODEL: PDB ENTRY 4KTQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 0.2M MGFORMATE, 0.1M REMARK 280 TRIS, PH 8.5, 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 30.15567 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 60.31133 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 60.31133 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 30.15567 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: 6890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 PHE A 647 REMARK 465 GLY A 648 REMARK 465 VAL A 649 REMARK 465 PRO A 650 REMARK 465 ARG A 651 REMARK 465 GLU A 652 REMARK 465 ALA A 653 REMARK 465 DA C 201 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 VAL A 654 CG1 CG2 REMARK 470 LEU A 657 CG CD1 CD2 REMARK 470 MET A 658 CG SD CE REMARK 470 ARG A 677 CG CD NE CZ NH1 NH2 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 O ASP A 732 O HOH A 849 1.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG A 392 OE2 GLU A 602 2545 2.03 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 DG B 108 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 111 C3' - O3' - P ANGL. DEV. = -15.5 DEGREES REMARK 500 DOC B 112 O3' - P - OP2 ANGL. DEV. = 14.9 DEGREES REMARK 500 DOC B 112 O3' - P - OP1 ANGL. DEV. = -23.4 DEGREES REMARK 500 DG C 211 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 328 146.44 -177.67 REMARK 500 ASP A 381 109.46 -161.48 REMARK 500 THR A 399 -163.29 -105.38 REMARK 500 VAL A 433 -72.19 -122.71 REMARK 500 HIS A 480 145.95 -179.74 REMARK 500 HIS A 526 136.58 177.83 REMARK 500 VAL A 586 -9.31 -160.20 REMARK 500 TRP A 645 41.84 -83.66 REMARK 500 ALA A 683 69.45 -60.29 REMARK 500 HIS A 784 -68.85 76.09 REMARK 500 TYR A 811 89.31 -164.29 REMARK 500 LYS A 831 44.53 -91.92 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 7 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 885 O REMARK 620 2 HOH A 886 O 89.6 REMARK 620 3 HOH A 887 O 90.6 89.9 REMARK 620 4 HOH A 888 O 88.3 90.3 178.9 REMARK 620 5 HOH A 889 O 90.8 179.5 89.8 90.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 7 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 2 O REMARK 620 2 HOH B 4 O 90.2 REMARK 620 3 HOH B 5 O 89.9 90.4 REMARK 620 4 HOH B 6 O 90.5 89.8 179.5 REMARK 620 5 HOH B 115 O 179.5 89.3 90.2 89.4 REMARK 620 6 HOH C 218 O 89.5 179.7 89.5 90.2 91.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 7 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 119 O REMARK 620 2 HOH C 1 O 179.4 REMARK 620 3 HOH C 4 O 90.4 89.2 REMARK 620 4 HOH C 221 O 89.3 90.3 90.6 REMARK 620 5 HOH C 222 O 90.4 90.0 89.9 179.5 REMARK 620 6 HOH C 223 O 90.4 90.1 179.2 89.6 90.0 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 FMT A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 836 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 837 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 838 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 839 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KTQ RELATED DB: PDB REMARK 900 RELATED ID: 3SV3 RELATED DB: PDB REMARK 900 RELATED ID: 3SYZ RELATED DB: PDB REMARK 900 RELATED ID: 3SZ2 RELATED DB: PDB DBREF 3SV4 A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 3SV4 B 101 112 PDB 3SV4 3SV4 101 112 DBREF 3SV4 C 201 216 PDB 3SV4 3SV4 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 3SV4 DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC B 112 30 HET FMT A 1 4 HET FMT A 833 4 HET FMT A 834 5 HET MG A 7 1 HET FMT A 835 5 HET FMT A 836 5 HET FMT A 837 5 HET FMT A 838 3 HET FMT A 839 3 HET MG B 7 1 HET FMT B 1 4 HET MG C 7 1 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM FMT FORMIC ACID HETNAM MG MAGNESIUM ION FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 FMT 9(C H2 O2) FORMUL 7 MG 3(MG 2+) FORMUL 16 HOH *320(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 GLU A 421 1 21 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 ALA A 521 1 7 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 TRP A 645 1 9 HELIX 17 17 PRO A 656 TYR A 671 1 16 HELIX 18 18 SER A 674 LEU A 682 1 9 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 GLY A 776 1 40 HELIX 23 23 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 PHE A 306 O ALA A 327 SHEET 1 B 2 ARG A 450 LEU A 451 0 SHEET 2 B 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 C 2 ARG A 563 ASN A 565 0 SHEET 2 C 2 SER A 575 SER A 577 -1 O SER A 575 N ASN A 565 SHEET 1 D 4 ARG A 778 GLN A 782 0 SHEET 2 D 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 D 4 TRP A 604 TYR A 611 -1 N LEU A 609 O LEU A 787 SHEET 4 D 4 VAL A 819 GLY A 824 -1 O GLY A 824 N LEU A 606 SHEET 1 E 2 TYR A 719 GLU A 721 0 SHEET 2 E 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK O3' DC B 111 P DOC B 112 1555 1555 1.60 LINK MG MG A 7 O HOH A 885 1555 1555 2.18 LINK MG MG A 7 O HOH A 886 1555 1555 2.18 LINK MG MG A 7 O HOH A 887 1555 1555 2.18 LINK MG MG A 7 O HOH A 888 1555 1555 2.18 LINK MG MG A 7 O HOH A 889 1555 1555 2.18 LINK O HOH B 2 MG MG B 7 1555 1555 2.18 LINK O HOH B 4 MG MG B 7 1555 1555 2.18 LINK O HOH B 5 MG MG B 7 1555 1555 2.18 LINK O HOH B 6 MG MG B 7 1555 1555 2.18 LINK MG MG B 7 O HOH B 115 1555 1555 2.18 LINK MG MG B 7 O HOH C 218 1555 1555 2.18 LINK O HOH B 119 MG MG C 7 1555 1555 2.18 LINK O HOH C 1 MG MG C 7 1555 1555 2.18 LINK O HOH C 4 MG MG C 7 1555 1555 2.18 LINK MG MG C 7 O HOH C 221 1555 1555 2.18 LINK MG MG C 7 O HOH C 222 1555 1555 2.18 LINK MG MG C 7 O HOH C 223 1555 1555 2.18 CISPEP 1 TRP A 299 PRO A 300 0 1.87 CISPEP 2 ASP A 578 PRO A 579 0 -1.58 SITE 1 AC1 2 ARG A 313 TRP A 318 SITE 1 AC2 2 HOH A 11 PHE A 724 SITE 1 AC3 5 ARG A 617 PHE A 632 GLY A 635 PRO A 816 SITE 2 AC3 5 GLU A 818 SITE 1 AC4 6 GLU A 786 HOH A 885 HOH A 886 HOH A 887 SITE 2 AC4 6 HOH A 888 HOH A 889 SITE 1 AC5 6 HOH A 207 PRO A 589 GLN A 592 ARG A 593 SITE 2 AC5 6 ARG A 596 SER A 829 SITE 1 AC6 6 HOH A 94 HOH A 151 HIS A 621 MET A 775 SITE 2 AC6 6 LEU A 802 ALA A 814 SITE 1 AC7 3 HOH A 108 LYS A 767 HOH A 865 SITE 1 AC8 8 HOH A 88 ASN A 485 SER A 486 ARG A 487 SITE 2 AC8 8 HOH A 874 DG C 211 DT C 212 HOH C 225 SITE 1 AC9 5 HOH A 22 HOH A 40 LYS A 354 ASP A 355 SITE 2 AC9 5 ARG A 563 SITE 1 BC1 6 HOH B 2 HOH B 4 HOH B 5 HOH B 6 SITE 2 BC1 6 HOH B 115 HOH C 218 SITE 1 BC2 5 GLU A 337 PRO A 338 TYR A 339 LYS A 340 SITE 2 BC2 5 DG B 101 SITE 1 BC3 6 HOH B 119 HOH C 1 HOH C 4 HOH C 221 SITE 2 BC3 6 HOH C 222 HOH C 223 CRYST1 108.388 108.388 90.467 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 0.009226 0.005327 0.000000 0.00000 SCALE2 0.000000 0.010653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011054 0.00000