HEADER TRANSFERASE/DNA 01-OCT-13 4C8O TITLE BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS TITLE 2 AQUATICUS WITH THE ARITIFICIAL BASE PAIR DNAM-D5SICS AT THE TITLE 3 POSTINSERTION SITE (SEQUENCE CONTEXT 2) 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; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: OPEN CONFORMATION OF ENZYME TRAPPED BY CRYSTAL COMPND 9 CONTACTS; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: 5'-D(*GP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3'; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: PRIMER; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: 5'-D(*TP*TP*CP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*CP)-3'; COMPND 17 CHAIN: C; COMPND 18 SYNONYM: TEMPLATE; COMPND 19 ENGINEERED: YES 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, DNA POLYMERASE, UNNATURAL BASE PAIR, KEYWDS 2 ARTIFICIAL BASE PAIR, 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 3 23-AUG-17 4C8O 1 REMARK ATOM REVDAT 2 25-DEC-13 4C8O 1 JRNL HETATM REVDAT 1 11-DEC-13 4C8O 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. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 66155 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3300 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 47.8939 - 5.0461 1.00 2792 157 0.1405 0.1638 REMARK 3 2 5.0461 - 4.0058 0.99 2684 140 0.1264 0.1411 REMARK 3 3 4.0058 - 3.4997 1.00 2686 126 0.1479 0.1761 REMARK 3 4 3.4997 - 3.1797 1.00 2655 149 0.1767 0.2097 REMARK 3 5 3.1797 - 2.9519 1.00 2619 141 0.2005 0.2320 REMARK 3 6 2.9519 - 2.7779 1.00 2662 136 0.2105 0.2274 REMARK 3 7 2.7779 - 2.6387 1.00 2590 189 0.2070 0.2504 REMARK 3 8 2.6387 - 2.5239 1.00 2638 127 0.2024 0.2721 REMARK 3 9 2.5239 - 2.4267 1.00 2617 125 0.1951 0.2105 REMARK 3 10 2.4267 - 2.3430 1.00 2661 118 0.1969 0.2371 REMARK 3 11 2.3430 - 2.2697 1.00 2579 137 0.1988 0.2238 REMARK 3 12 2.2697 - 2.2049 1.00 2606 146 0.2045 0.2482 REMARK 3 13 2.2049 - 2.1468 0.99 2615 143 0.2102 0.2596 REMARK 3 14 2.1468 - 2.0944 1.00 2595 131 0.2220 0.3116 REMARK 3 15 2.0944 - 2.0468 1.00 2598 130 0.2409 0.2872 REMARK 3 16 2.0468 - 2.0033 0.99 2615 133 0.2602 0.2966 REMARK 3 17 2.0033 - 1.9632 1.00 2593 127 0.2770 0.3009 REMARK 3 18 1.9632 - 1.9261 0.99 2596 130 0.3100 0.3227 REMARK 3 19 1.9261 - 1.8917 0.99 2576 146 0.3173 0.3133 REMARK 3 20 1.8917 - 1.8597 1.00 2556 137 0.3267 0.3788 REMARK 3 21 1.8597 - 1.8297 0.99 2624 129 0.3562 0.3890 REMARK 3 22 1.8297 - 1.8015 1.00 2551 131 0.3724 0.3759 REMARK 3 23 1.8015 - 1.7750 0.98 2572 147 0.4029 0.4166 REMARK 3 24 1.7750 - 1.7500 1.00 2575 125 0.4418 0.4286 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.57 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 4979 REMARK 3 ANGLE : 0.964 6857 REMARK 3 CHIRALITY : 0.037 748 REMARK 3 PLANARITY : 0.004 840 REMARK 3 DIHEDRAL : 16.052 1949 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 293 THROUGH 433 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.7832 -30.8150 26.7820 REMARK 3 T TENSOR REMARK 3 T11: 0.3028 T22: 0.5848 REMARK 3 T33: 0.3253 T12: 0.0599 REMARK 3 T13: 0.0135 T23: 0.0442 REMARK 3 L TENSOR REMARK 3 L11: 2.5358 L22: 1.1660 REMARK 3 L33: 2.9345 L12: -0.7131 REMARK 3 L13: -0.3510 L23: -0.8393 REMARK 3 S TENSOR REMARK 3 S11: -0.1266 S12: 0.0001 S13: 0.0491 REMARK 3 S21: 0.1944 S22: 0.2151 S23: 0.1995 REMARK 3 S31: -0.2034 S32: -0.9330 S33: -0.0758 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 434 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.2761 -22.6910 38.5906 REMARK 3 T TENSOR REMARK 3 T11: 0.3796 T22: 0.3531 REMARK 3 T33: 0.3715 T12: 0.0085 REMARK 3 T13: 0.0274 T23: 0.0488 REMARK 3 L TENSOR REMARK 3 L11: 1.7742 L22: 1.4140 REMARK 3 L33: 1.5473 L12: 0.9056 REMARK 3 L13: 0.3779 L23: 0.9626 REMARK 3 S TENSOR REMARK 3 S11: 0.0427 S12: 0.1089 S13: 0.2466 REMARK 3 S21: -0.0404 S22: 0.0663 S23: -0.1103 REMARK 3 S31: -0.2431 S32: 0.1850 S33: -0.1264 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 589 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.9291 -32.5650 15.6503 REMARK 3 T TENSOR REMARK 3 T11: 0.2692 T22: 0.4293 REMARK 3 T33: 0.2905 T12: 0.0250 REMARK 3 T13: -0.0065 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 1.3138 L22: 0.6797 REMARK 3 L33: 1.8441 L12: 0.1624 REMARK 3 L13: -0.0510 L23: -0.5802 REMARK 3 S TENSOR REMARK 3 S11: -0.0716 S12: 0.2466 S13: 0.0542 REMARK 3 S21: -0.0131 S22: -0.0104 S23: -0.1280 REMARK 3 S31: 0.0426 S32: 0.2604 S33: 0.1038 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND (RESID 102 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.1986 -13.7876 36.5147 REMARK 3 T TENSOR REMARK 3 T11: 0.6287 T22: 0.4229 REMARK 3 T33: 0.3962 T12: 0.0346 REMARK 3 T13: 0.0063 T23: 0.0307 REMARK 3 L TENSOR REMARK 3 L11: 4.4969 L22: 2.0149 REMARK 3 L33: 5.3112 L12: 1.9725 REMARK 3 L13: -2.3293 L23: 0.4624 REMARK 3 S TENSOR REMARK 3 S11: -0.3012 S12: 1.0108 S13: -0.0265 REMARK 3 S21: -0.4996 S22: 0.2496 S23: -0.1550 REMARK 3 S31: -0.1630 S32: -0.6300 S33: 0.0979 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN C AND (RESID 204 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.0797 -14.4025 35.2181 REMARK 3 T TENSOR REMARK 3 T11: 0.6577 T22: 0.5769 REMARK 3 T33: 0.4458 T12: 0.1416 REMARK 3 T13: 0.0165 T23: 0.0647 REMARK 3 L TENSOR REMARK 3 L11: 6.0508 L22: 7.0638 REMARK 3 L33: 5.3865 L12: -1.9020 REMARK 3 L13: -2.0384 L23: 4.5683 REMARK 3 S TENSOR REMARK 3 S11: 0.5078 S12: 1.3289 S13: 0.3636 REMARK 3 S21: -0.9405 S22: -0.5467 S23: -0.0947 REMARK 3 S31: -0.7116 S32: -0.7023 S33: -0.1107 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 4C8O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1290058560. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00001 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66214 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 48.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.990 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 (%): 48.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M MES PH REMARK 280 6.5, 30% W/V PEG 5000MME REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 101.80100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 101.80100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 32.40100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.59250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.40100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.59250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 101.80100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.40100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.59250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 101.80100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.40100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.59250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: 6180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.1 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C2006 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 DT C 202 REMARK 465 DT C 203 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 HE21 GLN A 613 O2 SO4 A 1834 1.57 REMARK 500 OD2 ASP A 759 O HOH A 2193 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC C 210 C2' DC C 210 C1' 0.066 REMARK 500 DC C 210 O4' DC C 210 C4' -0.071 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 DC C 210 C3' - C2' - C1' ANGL. DEV. = -10.8 DEGREES REMARK 500 DC C 210 O4' - C1' - C2' ANGL. DEV. = 6.9 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 LEU A 294 71.15 55.16 REMARK 500 ASP A 381 109.12 -166.82 REMARK 500 PRO A 382 0.11 -66.85 REMARK 500 VAL A 433 -70.09 -118.16 REMARK 500 ILE A 503 -89.22 -129.26 REMARK 500 HIS A 561 77.51 -113.85 REMARK 500 ARG A 636 -155.62 -98.93 REMARK 500 GLU A 734 62.45 -115.46 REMARK 500 HIS A 784 -124.88 50.25 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 A1835 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A3001 O REMARK 620 2 HOH A3003 O 89.7 REMARK 620 3 HOH A3005 O 89.8 89.2 REMARK 620 4 HOH A3004 O 90.2 90.4 179.6 REMARK 620 5 HOH A3006 O 89.9 179.1 90.1 90.4 REMARK 620 6 HOH A3002 O 179.3 90.9 90.2 89.8 89.5 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 SO4 A 1833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1836 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1837 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1838 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1839 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1840 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1841 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS C 1216 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4C8J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM REMARK 900 THERMUS AQUATICUS IN AN OPEN BINARY COMPLEX WITH D5SICS AS REMARK 900 TEMPLATING NUCLEOTIDE REMARK 900 RELATED ID: 4C8K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM REMARK 900 THERMUS AQUATICUS IN A PARTIALLY CLOSED COMPLEX WITH THE ARTIFICIAL REMARK 900 BASE PAIR D5SICS- DNAMTP REMARK 900 RELATED ID: 4C8L RELATED DB: PDB REMARK 900 BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM REMARK 900 THERMUS AQUATICUS WITH THE ARTIFICIAL BASE PAIR DNAM-D5SICS AT THE REMARK 900 POSTINSERTION SITE (SEQUENCE CONTEXT 1) REMARK 900 RELATED ID: 4C8M RELATED DB: PDB REMARK 900 BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM REMARK 900 THERMUS AQUATICUS WITH THE ARITIFICIAL BASE PAIR D5SICS-DNAM AT THE REMARK 900 POSTINSERTION SITE (SEQUENCE CONTEXT 2) REMARK 900 RELATED ID: 4C8N RELATED DB: PDB REMARK 900 BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM REMARK 900 THERMUS AQUATICUS WITH THE ARITIFICIAL BASE PAIR DNAM-D5SICS AT THE REMARK 900 POSTINSERTION SITE (SEQUENCE CONTEXT 3) REMARK 999 REMARK 999 SEQUENCE REMARK 999 5'-TT OF THE TEMPLATE IS NOT RESOLVED IN THE STRUCTURE DBREF 4C8O A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4C8O B 102 112 PDB 4C8O 4C8O 102 112 DBREF 4C8O C 202 215 PDB 4C8O 4C8O 202 215 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 11 DG DC DC DA DC DG DG DC DG DC LHO SEQRES 1 C 14 DT DT DC BMN DG DC DG DC DC DG DT DG DG SEQRES 2 C 14 DC HET LHO B 112 40 HET BMN C 205 39 HET SO4 A1833 5 HET SO4 A1834 5 HET MG A1835 1 HET CL A1836 1 HET SO4 A1837 5 HET SO4 A1838 5 HET SO4 A1839 5 HET SO4 A1840 5 HET SO4 A1841 5 HET TRS C1216 20 HETNAM LHO 2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 LHO PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE HETNAM BMN (1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)- HETNAM 2 BMN 5-O-PHOSPHONO-D-ERYTHRO-PENTITOL HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 LHO C15 H18 N O6 P S FORMUL 3 BMN C16 H19 O7 P FORMUL 4 SO4 7(O4 S 2-) FORMUL 6 MG MG 2+ FORMUL 7 CL CL 1- FORMUL 13 TRS C4 H12 N O3 1+ FORMUL 14 HOH *236(H2 O) HELIX 1 1 GLU A 315 ALA A 319 5 5 HELIX 2 2 GLU A 337 ARG A 343 1 7 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 ALA A 521 1 7 HELIX 12 12 HIS A 526 ILE A 546 1 21 HELIX 13 13 ASP A 547 LEU A 552 1 6 HELIX 14 14 ASN A 580 ILE A 584 5 5 HELIX 15 15 THR A 588 ARG A 596 1 9 HELIX 16 16 GLN A 613 GLY A 624 1 12 HELIX 17 17 ASP A 625 GLU A 634 1 10 HELIX 18 18 ASP A 637 GLY A 648 1 12 HELIX 19 19 PRO A 650 VAL A 654 5 5 HELIX 20 20 ASP A 655 VAL A 669 1 15 HELIX 21 21 SER A 674 ALA A 683 1 10 HELIX 22 22 PRO A 685 PHE A 700 1 16 HELIX 23 23 PHE A 700 GLY A 718 1 19 HELIX 24 24 PRO A 731 ALA A 735 5 5 HELIX 25 25 VAL A 737 MET A 775 1 39 HELIX 26 26 ARG A 795 GLY A 809 1 15 HELIX 27 27 ASP A 826 GLU A 832 1 7 SHEET 1 AA 4 GLU A 296 ALA A 297 0 SHEET 2 AA 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 AA 4 LEU A 321 ARG A 328 -1 O ALA A 326 N HIS A 333 SHEET 4 AA 4 PHE A 306 LEU A 311 -1 O PHE A 306 N ALA A 327 SHEET 1 AB 2 ARG A 450 LEU A 451 0 SHEET 2 AB 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 AC 2 ARG A 563 ASN A 565 0 SHEET 2 AC 2 SER A 575 SER A 577 -1 O SER A 575 N ASN A 565 SHEET 1 AD 4 ARG A 778 VAL A 783 0 SHEET 2 AD 4 GLU A 786 PRO A 792 -1 O GLU A 786 N VAL A 783 SHEET 3 AD 4 TRP A 604 TYR A 611 -1 O LEU A 605 N ALA A 791 SHEET 4 AD 4 VAL A 819 GLY A 824 -1 O GLU A 820 N ASP A 610 SHEET 1 AE 2 TYR A 719 GLU A 721 0 SHEET 2 AE 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK MG MG A1835 O HOH A3001 1555 1555 2.18 LINK MG MG A1835 O HOH A3003 1555 1555 2.18 LINK MG MG A1835 O HOH A3005 1555 1555 2.18 LINK MG MG A1835 O HOH A3004 1555 1555 2.18 LINK MG MG A1835 O HOH A3006 1555 1555 2.18 LINK MG MG A1835 O HOH A3002 1555 1555 2.18 LINK O3' DC B 111 P LHO B 112 1555 1555 1.60 LINK O3' DC C 204 P BMN C 205 1555 1555 1.61 LINK O3' BMN C 205 P DG C 206 1555 1555 1.61 CISPEP 1 TRP A 299 PRO A 300 0 2.41 CISPEP 2 ASP A 578 PRO A 579 0 1.13 SITE 1 AC1 1 ARG A 313 SITE 1 AC2 6 GLN A 613 HIS A 639 LYS A 663 PHE A 667 SITE 2 AC2 6 HOH A2150 HOH A2171 SITE 1 AC3 6 HOH A3001 HOH A3002 HOH A3003 HOH A3004 SITE 2 AC3 6 HOH A3005 HOH A3006 SITE 1 AC4 1 LYS A 314 SITE 1 AC5 3 VAL A 310 LEU A 311 ARG A 405 SITE 1 AC6 3 HOH A3003 DC B 103 HOH B2002 SITE 1 AC7 4 SER A 674 ALA A 675 HIS A 676 TYR A 686 SITE 1 AC8 2 ARG A 431 ARG A 435 SITE 1 AC9 3 ARG A 393 ARG A 419 HOH A2038 SITE 1 BC1 3 DC B 106 DC C 209 DC C 210 CRYST1 64.802 99.185 203.602 90.00 90.00 90.00 C 2 2 21 8 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 0.015432 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004912 0.00000