HEADER TRANSFERASE/DNA 01-OCT-13 4C8K TITLE CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM TITLE 2 THERMUS AQUATICUS IN A PARTIALLY CLOSED COMPLEX WITH THE ARTIFICIAL TITLE 3 BASE PAIR D5SICS-DNAMTP 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*C*DOC)-3'; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: PRIMER'; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*AP*AP*C*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'; COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES; COMPND 17 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 NUCLEOTIDE, KEYWDS 2 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 4 20-DEC-23 4C8K 1 REMARK LINK REVDAT 3 23-AUG-17 4C8K 1 REMARK ATOM REVDAT 2 25-DEC-13 4C8K 1 JRNL ATOM REVDAT 1 11-DEC-13 4C8K 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. 2.17 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) : 2.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 16.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 3 NUMBER OF REFLECTIONS : 33357 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1671 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 48.6494 - 4.9664 1.00 3077 171 0.1570 0.1828 REMARK 3 2 4.9664 - 3.9426 1.00 2972 172 0.1415 0.1816 REMARK 3 3 3.9426 - 3.4444 0.87 2569 141 0.1669 0.2092 REMARK 3 4 3.4444 - 3.1295 1.00 2936 142 0.1900 0.2556 REMARK 3 5 3.1295 - 2.9052 1.00 2936 176 0.2226 0.2581 REMARK 3 6 2.9052 - 2.7339 1.00 2929 151 0.2094 0.2663 REMARK 3 7 2.7339 - 2.5970 1.00 2906 161 0.2081 0.2406 REMARK 3 8 2.5970 - 2.4840 1.00 2910 154 0.2099 0.2524 REMARK 3 9 2.4840 - 2.3884 1.00 2948 129 0.2105 0.2587 REMARK 3 10 2.3884 - 2.3060 1.00 2914 146 0.2261 0.2901 REMARK 3 11 2.3060 - 2.2339 0.98 987 56 0.2991 0.3744 REMARK 3 12 2.2339 - 2.1700 0.99 1602 72 0.3646 0.3339 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.15 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 : 0.007 5049 REMARK 3 ANGLE : 0.870 6944 REMARK 3 CHIRALITY : 0.034 757 REMARK 3 PLANARITY : 0.004 824 REMARK 3 DIHEDRAL : 16.869 1970 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 293 THROUGH 433 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.8379 -45.8972 -17.8253 REMARK 3 T TENSOR REMARK 3 T11: 0.5005 T22: 0.2709 REMARK 3 T33: 0.3202 T12: -0.0537 REMARK 3 T13: 0.0543 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.9109 L22: 1.5411 REMARK 3 L33: 0.9151 L12: -0.5436 REMARK 3 L13: -0.2296 L23: -0.2120 REMARK 3 S TENSOR REMARK 3 S11: -0.1146 S12: -0.0046 S13: -0.3103 REMARK 3 S21: -0.1263 S22: -0.0190 S23: -0.1023 REMARK 3 S31: 0.3177 S32: 0.1056 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 434 THROUGH 633 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.0662 -16.9066 -3.4864 REMARK 3 T TENSOR REMARK 3 T11: 0.3830 T22: 0.2470 REMARK 3 T33: 0.4244 T12: -0.0692 REMARK 3 T13: -0.0051 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.8468 L22: 0.2337 REMARK 3 L33: 1.4157 L12: 0.1014 REMARK 3 L13: -0.2202 L23: 0.1936 REMARK 3 S TENSOR REMARK 3 S11: 0.0102 S12: 0.0002 S13: 0.3215 REMARK 3 S21: -0.0727 S22: 0.0466 S23: -0.0099 REMARK 3 S31: -0.2036 S32: 0.0631 S33: 0.0006 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 634 THROUGH 671 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.5903 -14.2162 -7.0660 REMARK 3 T TENSOR REMARK 3 T11: 1.0082 T22: 0.6912 REMARK 3 T33: 0.7531 T12: 0.1189 REMARK 3 T13: 0.0071 T23: 0.1112 REMARK 3 L TENSOR REMARK 3 L11: 0.0543 L22: 0.0394 REMARK 3 L33: 0.1205 L12: 0.0434 REMARK 3 L13: 0.1126 L23: 0.0774 REMARK 3 S TENSOR REMARK 3 S11: -0.0833 S12: 0.0236 S13: -0.0001 REMARK 3 S21: -0.1453 S22: 0.0149 S23: 0.0269 REMARK 3 S31: -0.7811 S32: -0.3824 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESID 672 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.7319 -28.1173 -11.6038 REMARK 3 T TENSOR REMARK 3 T11: 0.3663 T22: 0.3037 REMARK 3 T33: 0.2872 T12: -0.0835 REMARK 3 T13: -0.0376 T23: 0.0229 REMARK 3 L TENSOR REMARK 3 L11: 1.3530 L22: 0.4536 REMARK 3 L33: 1.1973 L12: -0.0253 REMARK 3 L13: -0.4913 L23: -0.1967 REMARK 3 S TENSOR REMARK 3 S11: -0.0911 S12: 0.0561 S13: 0.0144 REMARK 3 S21: -0.0434 S22: 0.0083 S23: 0.0730 REMARK 3 S31: 0.0084 S32: -0.2104 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND (RESID 101 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.7262 -26.2851 5.3644 REMARK 3 T TENSOR REMARK 3 T11: 0.3654 T22: 0.4789 REMARK 3 T33: 0.4120 T12: -0.0268 REMARK 3 T13: 0.0024 T23: 0.0468 REMARK 3 L TENSOR REMARK 3 L11: 0.0178 L22: 0.0739 REMARK 3 L33: 0.2176 L12: 0.0716 REMARK 3 L13: -0.1024 L23: -0.1813 REMARK 3 S TENSOR REMARK 3 S11: -0.2597 S12: 0.3216 S13: -0.0649 REMARK 3 S21: 0.3479 S22: -0.1570 S23: 0.1643 REMARK 3 S31: -0.5642 S32: 0.5374 S33: -0.0193 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN C AND (RESID 203 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.9850 -26.7946 5.7586 REMARK 3 T TENSOR REMARK 3 T11: 0.3812 T22: 0.3822 REMARK 3 T33: 0.3428 T12: 0.0023 REMARK 3 T13: -0.0141 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.0584 L22: 0.3712 REMARK 3 L33: 0.4301 L12: 0.0221 REMARK 3 L13: -0.2645 L23: 0.3517 REMARK 3 S TENSOR REMARK 3 S11: -0.3342 S12: -0.0866 S13: -0.1757 REMARK 3 S21: 0.1176 S22: 0.2414 S23: -0.1497 REMARK 3 S31: 0.1889 S32: 0.1375 S33: 0.0001 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES 643-660 HAVE HIGH B- -FACTORS REMARK 4 REMARK 4 4C8K 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_1290058437. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.99987 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 : 34375 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.160 REMARK 200 RESOLUTION RANGE LOW (A) : 48.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.470 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3M8S REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% W/V PEG 8000, 100MM TRIS PH 7.0, REMARK 280 200MM MAGNESIUM FORMIAT 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 30.36867 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 60.73733 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 60.73733 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 30.36867 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: 6390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.7 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 DA C 201 REMARK 465 DA C 202 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. = 2.6 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 111 C3' - O3' - P ANGL. DEV. = -9.2 DEGREES REMARK 500 DOC B 112 O3' - P - OP2 ANGL. DEV. = 15.1 DEGREES REMARK 500 DOC B 112 O3' - P - OP1 ANGL. DEV. = -13.8 DEGREES REMARK 500 DG C 214 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 ASP A 381 111.00 -163.85 REMARK 500 PRO A 382 1.09 -68.18 REMARK 500 TYR A 545 -59.18 -125.39 REMARK 500 VAL A 586 -22.47 -152.16 REMARK 500 HIS A 784 -64.42 69.43 REMARK 500 TYR A 811 98.86 -161.76 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 BMR A1834 O3C REMARK 620 2 BMR A1834 O2B 74.8 REMARK 620 3 BMR A1834 O1A 95.6 72.7 REMARK 620 4 HOH A2085 O 164.9 110.0 73.1 REMARK 620 5 HOH A2086 O 78.9 147.4 91.3 91.2 REMARK 620 6 HOH A2111 O 98.9 100.1 161.6 94.4 102.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1113 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2004 O REMARK 620 2 HOH B2005 O 89.4 REMARK 620 3 HOH B2008 O 89.4 91.5 REMARK 620 4 HOH B2016 O 90.8 179.4 89.1 REMARK 620 5 HOH B2017 O 179.7 90.3 90.4 89.5 REMARK 620 6 HOH B2018 O 90.2 88.9 179.4 90.6 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 GOL A 1833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMR 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 MG B 1113 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 1217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS C 1218 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: 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 900 RELATED ID: 4C8O 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 2) REMARK 999 REMARK 999 SEQUENCE REMARK 999 5'-AA OF THE TEMPLATE IS NOT RESOLVED IN THE STRUCTURE DBREF 4C8K A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4C8K B 101 112 PDB 4C8K 4C8K 101 112 DBREF 4C8K C 201 216 PDB 4C8K 4C8K 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 4C8K DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC B 112 30 HET LHO C 204 39 HET GOL A1833 14 HET BMR A1834 49 HET MG A1835 1 HET MG B1113 1 HET GOL C1217 14 HET TRS C1218 20 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM LHO 2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 LHO PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE HETNAM GOL GLYCEROL HETNAM BMR ((2R,3S,5R)-3-HYDROXY-5-(3-METHOXYNAPHTHALEN-2-YL) HETNAM 2 BMR METHYL-TETRAHYDROGEN-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN BMR DNAM-TRIPHOSPHATE HETSYN TRS TRIS BUFFER FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 3 LHO C15 H18 N O6 P S FORMUL 4 GOL 2(C3 H8 O3) FORMUL 5 BMR C16 H21 O13 P3 FORMUL 6 MG 2(MG 2+) FORMUL 9 TRS C4 H12 N O3 1+ FORMUL 10 HOH *144(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 ALA A 521 1 7 HELIX 12 12 LEU A 522 HIS A 526 5 5 HELIX 13 13 PRO A 527 TYR A 545 1 19 HELIX 14 14 PRO A 548 LEU A 552 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 ASP A 655 TYR A 671 1 17 HELIX 20 20 SER A 674 LEU A 682 1 9 HELIX 21 21 PRO A 685 PHE A 700 1 16 HELIX 22 22 PHE A 700 GLY A 718 1 19 HELIX 23 23 VAL A 737 GLU A 774 1 38 HELIX 24 24 ARG A 795 GLY A 809 1 15 HELIX 25 25 ASP A 826 GLU A 832 1 7 SHEET 1 AA 4 GLU A 296 PRO A 298 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 GLN A 782 0 SHEET 2 AD 4 GLU A 786 PRO A 792 -1 O VAL A 788 N LEU A 780 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 O3' DC B 111 P DOC B 112 1555 1555 1.60 LINK O3' DC C 203 P LHO C 204 1555 1555 1.61 LINK O3' LHO C 204 P DG C 205 1555 1555 1.61 LINK O3C BMR A1834 MG MG A1835 1555 1555 2.37 LINK O2B BMR A1834 MG MG A1835 1555 1555 2.10 LINK O1A BMR A1834 MG MG A1835 1555 1555 2.32 LINK MG MG A1835 O HOH A2085 1555 1555 2.08 LINK MG MG A1835 O HOH A2086 1555 1555 2.08 LINK MG MG A1835 O HOH A2111 1555 1555 2.08 LINK MG MG B1113 O HOH B2004 1555 1555 2.18 LINK MG MG B1113 O HOH B2005 1555 1555 2.18 LINK MG MG B1113 O HOH B2008 1555 1555 2.18 LINK MG MG B1113 O HOH B2016 1555 1555 2.18 LINK MG MG B1113 O HOH B2017 1555 1555 2.18 LINK MG MG B1113 O HOH B2018 1555 1555 2.18 CISPEP 1 TRP A 299 PRO A 300 0 2.11 CISPEP 2 ASP A 578 PRO A 579 0 -0.58 SITE 1 AC1 2 PHE A 724 TYR A 811 SITE 1 AC2 14 ARG A 587 GLN A 613 HIS A 639 ARG A 659 SITE 2 AC2 14 ARG A 660 LYS A 663 PHE A 667 TYR A 671 SITE 3 AC2 14 MG A1835 HOH A2076 HOH A2085 HOH A2086 SITE 4 AC2 14 DOC B 112 DG C 205 SITE 1 AC3 4 BMR A1834 HOH A2085 HOH A2086 HOH A2111 SITE 1 AC4 6 HOH B2004 HOH B2005 HOH B2008 HOH B2016 SITE 2 AC4 6 HOH B2017 HOH B2018 SITE 1 AC5 4 DA B 102 DT C 212 DG C 213 DG C 214 SITE 1 AC6 2 DG C 205 DG C 206 CRYST1 115.039 115.039 91.106 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 0.008693 0.005019 0.000000 0.00000 SCALE2 0.000000 0.010037 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010976 0.00000