HEADER TRANSFERASE/DNA 23-OCT-13 4CCH TITLE CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I TITLE 2 FROM THERMUS AQUATICUS IN AN OPEN BINARY COMPLEX WITH TITLE 3 D5SICS AS TEMPLATING NUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KLENOW FRAGMENT, RESIDUES 293-832; COMPND 5 SYNONYM: TAQ POLYMERASE 1, LARGE FRAGMENT OF TAQ DNA POLYMERASE I; 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 OTHER_DETAILS: PRIMER'; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*AP*AP*CP*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP* COMPND 14 C)-3'; COMPND 15 CHAIN: C; COMPND 16 OTHER_DETAILS: TEMPLATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGDR11; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS TRANSFERASE-DNA COMPLEX, UNNATURAL NUCLEOTIDE, ARTIFICIAL KEYWDS 2 NUCLEOTIDE, BINARY COMPLEX, KLENTAQ EXPDTA X-RAY DIFFRACTION AUTHOR K.BETZ,D.A.MALYSHEV,T.LAVERGNE,W.WELTE,K.DIEDERICHS,F.E.ROMESBERG, AUTHOR 2 A.MARX REVDAT 2 25-DEC-13 4CCH 1 JRNL HETATM REVDAT 1 11-DEC-13 4CCH 0 JRNL AUTH K.BETZ,D.A.MALYSHEV,T.LAVERGNE,W.WELTE,K.DIEDERICHS, JRNL AUTH 2 F.E.ROMESBERG,A.MARX JRNL TITL STRUCTURAL INSIGHTS INTO DNA REPLICATION WITHOUT HYDROGEN JRNL TITL 2 BONDS. JRNL REF J.AM.CHEM.SOC. V. 135 18637 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 24283923 JRNL DOI 10.1021/JA409609J REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 2.550 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.526 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.35 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.87 REMARK 3 NUMBER OF REFLECTIONS : 22879 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.2098 REMARK 3 R VALUE (WORKING SET) : 0.2070 REMARK 3 FREE R VALUE : 0.2608 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.3 REMARK 3 FREE R VALUE TEST SET COUNT : 2303 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 43.5320 - 6.4193 1.00 2566 152 0.1505 0.2133 REMARK 3 2 6.4193 - 5.0977 1.00 2599 145 0.1669 0.2250 REMARK 3 3 5.0977 - 4.4540 1.00 2595 116 0.1545 0.2455 REMARK 3 4 4.4540 - 4.0471 1.00 2564 164 0.1594 0.2022 REMARK 3 5 4.0471 - 3.7572 1.00 2548 162 0.1807 0.2617 REMARK 3 6 3.7572 - 3.5358 1.00 2597 152 0.1987 0.2414 REMARK 3 7 3.5358 - 3.3588 1.00 2578 131 0.2181 0.2769 REMARK 3 8 3.3588 - 3.2126 1.00 2576 153 0.2288 0.2757 REMARK 3 9 3.2126 - 3.0890 1.00 2610 108 0.2373 0.2449 REMARK 3 10 3.0890 - 2.9824 1.00 2561 172 0.2615 0.2916 REMARK 3 11 2.9824 - 2.8892 1.00 2606 139 0.2799 0.3396 REMARK 3 12 2.8892 - 2.8066 1.00 2591 120 0.2964 0.3468 REMARK 3 13 2.8066 - 2.7328 1.00 2580 160 0.2940 0.3349 REMARK 3 14 2.7328 - 2.6661 1.00 2524 135 0.3375 0.3802 REMARK 3 15 2.6661 - 2.6055 1.00 2592 147 0.3439 0.3782 REMARK 3 16 2.6055 - 2.5500 0.99 2569 147 0.3483 0.3551 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.42 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.005 4883 REMARK 3 ANGLE : 0.770 6708 REMARK 3 CHIRALITY : 0.032 735 REMARK 3 PLANARITY : 0.003 801 REMARK 3 DIHEDRAL : 16.381 1900 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 295 THROUGH 433 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.4654 -45.2876 -17.8884 REMARK 3 T TENSOR REMARK 3 T11: 0.8382 T22: 0.2852 REMARK 3 T33: 0.6037 T12: 0.0505 REMARK 3 T13: 0.1391 T23: 0.0571 REMARK 3 L TENSOR REMARK 3 L11: 2.4497 L22: 2.2181 REMARK 3 L33: 1.7502 L12: 0.3190 REMARK 3 L13: 0.5765 L23: -0.8985 REMARK 3 S TENSOR REMARK 3 S11: 0.0357 S12: 0.1497 S13: -0.7914 REMARK 3 S21: -0.2653 S22: -0.1808 S23: -0.2805 REMARK 3 S31: 0.9350 S32: 0.3353 S33: 0.0987 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 434 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.4497 -15.3636 0.6713 REMARK 3 T TENSOR REMARK 3 T11: 0.6039 T22: 0.3211 REMARK 3 T33: 0.6462 T12: -0.1642 REMARK 3 T13: 0.1270 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 1.6495 L22: 0.1866 REMARK 3 L33: 1.2561 L12: 0.1560 REMARK 3 L13: -0.0088 L23: -0.4533 REMARK 3 S TENSOR REMARK 3 S11: 0.0052 S12: -0.2669 S13: 0.6854 REMARK 3 S21: -0.0530 S22: 0.0134 S23: -0.1743 REMARK 3 S31: -0.4091 S32: 0.2443 S33: -0.0014 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 589 THROUGH 700 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.2117 -18.4397 -8.2613 REMARK 3 T TENSOR REMARK 3 T11: 0.6113 T22: 0.5304 REMARK 3 T33: 0.7555 T12: 0.0796 REMARK 3 T13: 0.1603 T23: 0.0404 REMARK 3 L TENSOR REMARK 3 L11: 4.0325 L22: 2.0476 REMARK 3 L33: 4.2054 L12: 2.6752 REMARK 3 L13: 0.0155 L23: -0.5276 REMARK 3 S TENSOR REMARK 3 S11: 0.2387 S12: -0.6521 S13: 1.1539 REMARK 3 S21: 0.3585 S22: -0.1772 S23: 0.3134 REMARK 3 S31: -0.3894 S32: -1.2699 S33: -0.2290 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESID 701 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.0678 -29.0670 -15.4419 REMARK 3 T TENSOR REMARK 3 T11: 0.4641 T22: 0.3969 REMARK 3 T33: 0.3690 T12: -0.1058 REMARK 3 T13: 0.0955 T23: 0.0930 REMARK 3 L TENSOR REMARK 3 L11: 1.5265 L22: 0.7801 REMARK 3 L33: 2.7520 L12: 0.2899 REMARK 3 L13: -0.5046 L23: -0.6235 REMARK 3 S TENSOR REMARK 3 S11: 0.0137 S12: 0.2457 S13: 0.0272 REMARK 3 S21: -0.1265 S22: -0.0595 S23: -0.1542 REMARK 3 S31: 0.0949 S32: -0.5388 S33: 0.0225 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND (RESID 101 THROUGH 106 ) REMARK 3 ORIGIN FOR THE GROUP (A): 47.1068 -30.9569 7.2199 REMARK 3 T TENSOR REMARK 3 T11: 0.4393 T22: 0.4757 REMARK 3 T33: 0.7099 T12: 0.0125 REMARK 3 T13: -0.0748 T23: 0.1665 REMARK 3 L TENSOR REMARK 3 L11: 9.9494 L22: 6.0972 REMARK 3 L33: 1.1317 L12: 1.1891 REMARK 3 L13: -1.2462 L23: 1.7188 REMARK 3 S TENSOR REMARK 3 S11: -0.6443 S12: 0.9450 S13: -0.1941 REMARK 3 S21: 0.4971 S22: -0.1346 S23: -1.4075 REMARK 3 S31: -0.0248 S32: 0.2526 S33: 0.7326 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN B AND (RESID 107 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.4023 -19.6568 3.5045 REMARK 3 T TENSOR REMARK 3 T11: 0.4187 T22: 0.1996 REMARK 3 T33: 0.4245 T12: -0.0442 REMARK 3 T13: 0.1282 T23: 0.0168 REMARK 3 L TENSOR REMARK 3 L11: 7.0119 L22: 0.4247 REMARK 3 L33: 5.4068 L12: -1.1473 REMARK 3 L13: 5.5070 L23: -0.3992 REMARK 3 S TENSOR REMARK 3 S11: -0.0150 S12: -0.5078 S13: 0.4363 REMARK 3 S21: -0.0101 S22: 0.0124 S23: 0.2635 REMARK 3 S31: -0.1995 S32: -0.3827 S33: -0.0465 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN C AND (RESID 205 THROUGH 210 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.7962 -26.5491 -1.6988 REMARK 3 T TENSOR REMARK 3 T11: 0.4324 T22: 0.3553 REMARK 3 T33: 0.3125 T12: -0.0829 REMARK 3 T13: 0.1759 T23: 0.0629 REMARK 3 L TENSOR REMARK 3 L11: 2.4482 L22: 3.0927 REMARK 3 L33: 3.5204 L12: -2.1147 REMARK 3 L13: 0.7441 L23: 1.3999 REMARK 3 S TENSOR REMARK 3 S11: 0.3584 S12: 0.0007 S13: 0.7225 REMARK 3 S21: 0.1820 S22: 0.0646 S23: -0.0361 REMARK 3 S31: -0.3198 S32: -0.2163 S33: -0.3795 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN C AND (RESID 211 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 47.5741 -26.0227 12.6498 REMARK 3 T TENSOR REMARK 3 T11: 0.4440 T22: 0.5113 REMARK 3 T33: 0.5602 T12: -0.1064 REMARK 3 T13: -0.1538 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 2.0613 L22: 6.6058 REMARK 3 L33: 1.6039 L12: -3.6806 REMARK 3 L13: -1.8170 L23: 3.2284 REMARK 3 S TENSOR REMARK 3 S11: -0.5042 S12: -0.5192 S13: 0.4284 REMARK 3 S21: 1.1517 S22: 0.6202 S23: -0.6054 REMARK 3 S31: 0.0775 S32: 0.6390 S33: -0.1644 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE N-TERMINAL AMINO ACID 293 AND THE LOOP BETWEEN REMARK 3 RESIDUES 647-659 ARE NOT MODELLED DUE TO DISORDER REMARK 4 REMARK 4 4CCH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-OCT-13. REMARK 100 THE PDBE ID CODE IS EBI-58793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI( REMARK 200 111) MONOCHROMATOR REMARK 200 OPTICS : DYNAMICALLY BENDABLE REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL (PILATUS 6M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22906 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.55 REMARK 200 RESOLUTION RANGE LOW (A) : 49.50 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.0 REMARK 200 R MERGE (I) : 0.20 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.16 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.1 REMARK 200 R MERGE FOR SHELL (I) : 1.44 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.65 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V PEG 8000, 0.1M TRIS PH REMARK 280 8.0, 0.2M MAGNESIUM FORMATE, 20% GLYCEROL 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 30.51233 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 61.02467 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 61.02467 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 30.51233 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: 6250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.5 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 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 VAL A 654 REMARK 465 ASP A 655 REMARK 465 PRO A 656 REMARK 465 LEU A 657 REMARK 465 MET A 658 REMARK 465 DA C 201 REMARK 465 DA C 202 REMARK 465 DC C 203 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. = 2.8 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DOC B 112 O3' - P - O5' ANGL. DEV. = 17.5 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 ALA A 323 149.82 -170.01 REMARK 500 ASP A 381 109.87 -166.56 REMARK 500 VAL A 433 -68.13 -127.26 REMARK 500 ASP A 496 -57.99 -124.50 REMARK 500 ASN A 583 37.13 -140.70 REMARK 500 VAL A 586 -23.29 -148.04 REMARK 500 ARG A 587 -70.11 -75.74 REMARK 500 TRP A 645 30.82 -95.23 REMARK 500 MET A 646 10.80 -143.70 REMARK 500 ASP A 732 23.11 -75.26 REMARK 500 HIS A 784 -63.55 68.35 REMARK 500 TYR A 811 91.79 -160.33 REMARK 500 LEU A 813 -162.69 -100.03 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 B1112 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2012 O REMARK 620 2 HOH B2008 O 89.9 REMARK 620 3 HOH B2011 O 179.3 90.7 REMARK 620 4 HOH B2013 O 88.3 90.4 92.0 REMARK 620 5 HOH B2009 O 90.6 179.5 88.7 89.5 REMARK 620 6 HOH B2010 O 90.9 89.3 88.9 179.1 90.8 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 A1833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A1834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A1835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1112 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C1217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A1836 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE THREE 5'-NUCLEOTIDES (AAC) OF THE TEMPLATE ARE NOT REMARK 999 RESOLVED IN THE STRUCTURE DBREF 4CCH A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4CCH B 101 112 PDB 4CCH 4CCH 101 112 DBREF 4CCH C 201 216 PDB 4CCH 4CCH 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 DC LHO DG DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC MODRES 4CCH DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE MODRES 4CCH LHO C 204 DA MODIFIED ADENOSINE HET DOC B 112 30 HET LHO C 204 38 HET FMT A1833 5 HET FMT A1834 5 HET FMT A1835 4 HET MG B1112 1 HET GOL C1217 14 HET FMT A1836 4 HETNAM LHO 2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 LHO PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)- HETNAM 3 LHO THIONE HETNAM MG MAGNESIUM ION HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETNAM FMT FORMIC ACID HETSYN GOL GLYCERIN FORMUL 4 LHO C15 H18 N O6 P S FORMUL 5 MG MG 2+ FORMUL 6 DOC C9 H14 N3 O6 P FORMUL 7 GOL C3 H8 O3 FORMUL 8 FMT 4(C H2 O2) FORMUL 9 HOH *122(H2 O) HELIX 1 1 GLU A 337 LEU A 342 1 6 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 HIS A 526 TYR A 545 1 20 HELIX 12 12 PRO A 548 LEU A 552 5 5 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 ARG A 659 LEU A 670 1 12 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 MET A 775 1 39 HELIX 23 23 ARG A 795 GLY A 809 1 15 SHEET 1 AA 3 PHE A 306 LEU A 311 0 SHEET 2 AA 3 LEU A 321 ARG A 328 -1 N LEU A 322 O VAL A 310 SHEET 3 AA 3 ARG A 331 ARG A 334 -1 O ARG A 331 N ARG A 328 SHEET 1 AB 2 ARG A 563 ASN A 565 0 SHEET 2 AB 2 SER A 575 SER A 577 -1 O SER A 575 N ASN A 565 SHEET 1 AC 4 ARG A 778 GLN A 782 0 SHEET 2 AC 4 GLU A 786 PRO A 792 -1 O VAL A 788 N LEU A 780 SHEET 3 AC 4 TRP A 604 TYR A 611 -1 O LEU A 605 N ALA A 791 SHEET 4 AC 4 VAL A 819 GLY A 824 -1 O GLU A 820 N ASP A 610 SHEET 1 AD 2 TYR A 719 GLU A 721 0 SHEET 2 AD 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 B1112 O HOH B2012 1555 1555 2.18 LINK MG MG B1112 O HOH B2008 1555 1555 2.18 LINK MG MG B1112 O HOH B2011 1555 1555 2.18 LINK MG MG B1112 O HOH B2013 1555 1555 2.18 LINK MG MG B1112 O HOH B2009 1555 1555 2.18 LINK MG MG B1112 O HOH B2010 1555 1555 2.18 LINK O3' LHO C 204 P DG C 205 1555 1555 1.61 CISPEP 1 TRP A 299 PRO A 300 0 1.43 CISPEP 2 ASP A 578 PRO A 579 0 -5.02 SITE 1 AC1 2 PRO A 579 ASN A 580 SITE 1 AC2 3 ALA A 735 ARG A 736 VAL A 737 SITE 1 AC3 2 TRP A 428 HOH A2033 SITE 1 AC4 6 HOH B2008 HOH B2009 HOH B2010 HOH B2011 SITE 2 AC4 6 HOH B2012 HOH B2013 SITE 1 AC5 2 DG C 213 DG C 214 SITE 1 AC6 1 ARG A 313 CRYST1 114.262 114.262 91.537 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 0.008752 0.005053 0.000000 0.00000 SCALE2 0.000000 0.010106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010925 0.00000