HEADER TRANSFERASE/DNA 01-OCT-13 4C8L TITLE BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS TITLE 2 AQUATICUS WITH THE ARTIFICIAL BASE PAIR DNAM-D5SICS AT THE TITLE 3 POSTINSERTION SITE (SEQUENCE CONTEXT 1) 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(*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-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*GP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP)-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, DNA POLYMERASE, UNNATURAL BASE PAIR, KEYWDS 2 ARTIFICIAL BASE PAIR, 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 4C8L 1 REMARK LINK REVDAT 3 23-AUG-17 4C8L 1 REMARK ATOM REVDAT 2 25-DEC-13 4C8L 1 JRNL ATOM REVDAT 1 11-DEC-13 4C8L 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 21.660 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 74501 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7192 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 48.4132 - 5.2802 1.00 4519 253 0.1411 0.1429 REMARK 3 2 5.2802 - 4.1918 1.00 4549 244 0.1276 0.1564 REMARK 3 3 4.1918 - 3.6621 1.00 4517 234 0.1466 0.1706 REMARK 3 4 3.6621 - 3.3274 1.00 4534 224 0.1556 0.1678 REMARK 3 5 3.3274 - 3.0889 1.00 4587 237 0.1693 0.2093 REMARK 3 6 3.0889 - 2.9068 1.00 4554 244 0.1719 0.2080 REMARK 3 7 2.9068 - 2.7613 1.00 4483 290 0.1845 0.2207 REMARK 3 8 2.7613 - 2.6411 1.00 4482 292 0.1787 0.2081 REMARK 3 9 2.6411 - 2.5394 1.00 4594 204 0.1784 0.2082 REMARK 3 10 2.5394 - 2.4518 1.00 4516 223 0.1735 0.2373 REMARK 3 11 2.4518 - 2.3751 1.00 4632 208 0.1863 0.2242 REMARK 3 12 2.3751 - 2.3072 1.00 4476 231 0.1862 0.2099 REMARK 3 13 2.3072 - 2.2465 1.00 4602 244 0.1907 0.2442 REMARK 3 14 2.2465 - 2.1917 1.00 4517 265 0.2016 0.2134 REMARK 3 15 2.1917 - 2.1419 1.00 4521 235 0.2117 0.2327 REMARK 3 16 2.1419 - 2.0963 1.00 4588 214 0.2254 0.3020 REMARK 3 17 2.0963 - 2.0544 1.00 4507 252 0.2407 0.2968 REMARK 3 18 2.0544 - 2.0156 1.00 4557 216 0.2443 0.2734 REMARK 3 19 2.0156 - 1.9796 1.00 4564 226 0.2471 0.2719 REMARK 3 20 1.9796 - 1.9460 1.00 4542 228 0.2613 0.3148 REMARK 3 21 1.9460 - 1.9146 1.00 4585 258 0.2885 0.3476 REMARK 3 22 1.9146 - 1.8852 1.00 4472 256 0.3101 0.3322 REMARK 3 23 1.8852 - 1.8575 1.00 4584 230 0.3368 0.3780 REMARK 3 24 1.8575 - 1.8313 1.00 4525 226 0.3844 0.3807 REMARK 3 25 1.8313 - 1.8065 1.00 4587 231 0.4295 0.4016 REMARK 3 26 1.8065 - 1.7831 1.00 4472 260 0.4938 0.5507 REMARK 3 27 1.7831 - 1.7608 1.00 4449 266 0.5258 0.5166 REMARK 3 28 1.7608 - 1.7396 1.00 4640 226 0.5631 0.5264 REMARK 3 29 1.7396 - 1.7193 1.00 4446 243 0.5576 0.5733 REMARK 3 30 1.7193 - 1.7000 1.00 4633 232 0.6159 0.6326 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.47 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 : 0.011 5015 REMARK 3 ANGLE : 1.239 6895 REMARK 3 CHIRALITY : 0.052 749 REMARK 3 PLANARITY : 0.007 843 REMARK 3 DIHEDRAL : 16.068 1963 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 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.2100 -32.0765 27.3395 REMARK 3 T TENSOR REMARK 3 T11: 0.2595 T22: 0.5246 REMARK 3 T33: 0.3372 T12: -0.0185 REMARK 3 T13: -0.0061 T23: 0.1083 REMARK 3 L TENSOR REMARK 3 L11: 1.6738 L22: 0.7576 REMARK 3 L33: 1.8227 L12: -0.2983 REMARK 3 L13: 0.0991 L23: -0.4881 REMARK 3 S TENSOR REMARK 3 S11: -0.0125 S12: -0.0180 S13: -0.0230 REMARK 3 S21: 0.0272 S22: 0.2092 S23: 0.2444 REMARK 3 S31: -0.0428 S32: -0.8321 S33: -0.1628 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 453 THROUGH 562 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9056 -18.5768 42.4081 REMARK 3 T TENSOR REMARK 3 T11: 0.3640 T22: 0.3358 REMARK 3 T33: 0.3222 T12: -0.1200 REMARK 3 T13: 0.0187 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.8163 L22: 1.8743 REMARK 3 L33: 1.7243 L12: 0.4021 REMARK 3 L13: -0.0635 L23: -0.1154 REMARK 3 S TENSOR REMARK 3 S11: -0.0046 S12: 0.0056 S13: 0.2463 REMARK 3 S21: 0.0439 S22: 0.1131 S23: -0.0949 REMARK 3 S31: -0.3874 S32: 0.4260 S33: -0.0771 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 563 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.0072 -32.6286 17.0190 REMARK 3 T TENSOR REMARK 3 T11: 0.2304 T22: 0.3157 REMARK 3 T33: 0.2635 T12: -0.0041 REMARK 3 T13: -0.0065 T23: 0.0220 REMARK 3 L TENSOR REMARK 3 L11: 1.2455 L22: 0.8555 REMARK 3 L33: 2.9268 L12: 0.1217 REMARK 3 L13: -0.2594 L23: -0.8692 REMARK 3 S TENSOR REMARK 3 S11: 0.0423 S12: 0.2797 S13: 0.0625 REMARK 3 S21: -0.0377 S22: -0.0758 S23: -0.0883 REMARK 3 S31: 0.0938 S32: 0.3548 S33: 0.0242 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND (RESID 102 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.0570 -15.3834 34.9173 REMARK 3 T TENSOR REMARK 3 T11: 0.5518 T22: 0.3186 REMARK 3 T33: 0.4379 T12: -0.0045 REMARK 3 T13: 0.0287 T23: 0.0267 REMARK 3 L TENSOR REMARK 3 L11: 0.5190 L22: 0.6786 REMARK 3 L33: 1.4327 L12: -0.4290 REMARK 3 L13: -0.6278 L23: 0.6743 REMARK 3 S TENSOR REMARK 3 S11: 0.0988 S12: 0.2418 S13: 0.2214 REMARK 3 S21: 0.2624 S22: -0.1540 S23: 0.0143 REMARK 3 S31: -0.3799 S32: -0.3648 S33: -0.0758 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN C AND (RESID 203 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.4362 -15.8209 34.5662 REMARK 3 T TENSOR REMARK 3 T11: 0.4565 T22: 0.2520 REMARK 3 T33: 0.4595 T12: 0.0249 REMARK 3 T13: 0.0309 T23: 0.0271 REMARK 3 L TENSOR REMARK 3 L11: 2.2539 L22: 0.8784 REMARK 3 L33: 2.6806 L12: 0.9043 REMARK 3 L13: 0.2760 L23: 0.0053 REMARK 3 S TENSOR REMARK 3 S11: 0.0920 S12: 0.2650 S13: 0.4483 REMARK 3 S21: 0.1199 S22: 0.0793 S23: -0.0681 REMARK 3 S31: -0.2930 S32: -0.1719 S33: -0.2996 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 4C8L 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_1290058479. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-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) : 1.000000 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 : 74923 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 48.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.850 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3SZ2 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M MES PH REMARK 280 6.5, 28% 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 102.17050 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 102.17050 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 32.80700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.27150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.80700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.27150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 102.17050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.80700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.27150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 102.17050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.80700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.27150 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: 7070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 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 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 O3' DC C 210 C3' -0.038 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 B 111 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 207 O4' - C1' - N1 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 LEU A 294 75.76 62.98 REMARK 500 ASP A 381 113.73 -169.04 REMARK 500 THR A 399 -168.42 -108.69 REMARK 500 VAL A 433 -71.06 -119.10 REMARK 500 ILE A 503 -77.09 -86.76 REMARK 500 LYS A 508 -31.90 -131.01 REMARK 500 HIS A 526 134.06 -172.42 REMARK 500 HIS A 784 -121.61 47.90 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 A1841 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2128 O REMARK 620 2 HOH A2129 O 114.0 REMARK 620 3 DG B 110 OP1 89.1 156.4 REMARK 620 N 1 2 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 B2006 O REMARK 620 2 HOH B2008 O 89.9 REMARK 620 3 HOH B2025 O 89.6 178.1 REMARK 620 4 HOH B2026 O 178.7 89.2 91.4 REMARK 620 5 HOH B2027 O 92.8 90.1 88.1 88.2 REMARK 620 N 1 2 3 4 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 SO4 A 1834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1836 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1837 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1838 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1839 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1840 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1841 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1113 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 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: 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) DBREF 4C8L A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4C8L B 102 112 PDB 4C8L 4C8L 102 112 DBREF 4C8L C 203 215 PDB 4C8L 4C8L 203 215 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 DA DC DC DA DC DG DG DC DG DC LHO SEQRES 1 C 13 DA DG BMN DG DC DG DC DC DG DT DG DG DT HET LHO B 112 39 HET BMN C 205 39 HET GOL A1833 14 HET SO4 A1834 5 HET SO4 A1835 5 HET SO4 A1836 5 HET GOL A1837 14 HET GOL A1838 14 HET GOL A1839 14 HET GOL A1840 14 HET MG A1841 1 HET MG B1113 1 HET SO4 C1216 5 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 GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 LHO C15 H18 N O6 P S FORMUL 3 BMN C16 H19 O7 P FORMUL 4 GOL 5(C3 H8 O3) FORMUL 5 SO4 4(O4 S 2-) FORMUL 12 MG 2(MG 2+) FORMUL 15 HOH *279(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 LEU A 549 LEU A 552 5 4 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 GLY A 672 1 18 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 LYS A 831 1 6 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 O3' DC B 111 P LHO B 112 1555 1555 1.62 LINK O3' DG C 204 P BMN C 205 1555 1555 1.61 LINK O3' BMN C 205 P DG C 206 1555 1555 1.62 LINK MG MG A1841 O HOH A2128 1555 1555 2.99 LINK MG MG A1841 O HOH A2129 1555 1555 2.80 LINK MG MG A1841 OP1 DG B 110 1555 1555 2.24 LINK MG MG B1113 O HOH B2006 1555 1555 2.18 LINK MG MG B1113 O HOH B2008 1555 1555 2.17 LINK MG MG B1113 O HOH B2025 1555 1555 2.18 LINK MG MG B1113 O HOH B2026 1555 1555 2.17 LINK MG MG B1113 O HOH B2027 1555 1555 2.18 CISPEP 1 TRP A 299 PRO A 300 0 0.03 CISPEP 2 ASP A 578 PRO A 579 0 1.64 SITE 1 AC1 7 ARG A 587 GLU A 615 TYR A 671 HOH A2231 SITE 2 AC1 7 LHO B 112 DA C 203 DG C 204 SITE 1 AC2 2 ARG A 393 ARG A 419 SITE 1 AC3 4 HIS A 639 ARG A 659 LYS A 663 HOH A2184 SITE 1 AC4 4 SER A 674 ALA A 675 HIS A 676 TYR A 686 SITE 1 AC5 3 ASP A 371 ARG A 431 ARG A 435 SITE 1 AC6 6 TRP A 428 PHE A 724 TYR A 811 HOH A2064 SITE 2 AC6 6 HOH A2232 HOH A2233 SITE 1 AC7 6 ARG A 362 GLU A 465 HIS A 554 ARG A 556 SITE 2 AC7 6 HOH A2015 HOH A2234 SITE 1 AC8 4 TYR A 455 ALA A 458 GLU A 462 ARG A 593 SITE 1 AC9 4 HOH A2128 HOH A2129 DC B 109 DG B 110 SITE 1 BC1 5 HOH B2006 HOH B2008 HOH B2025 HOH B2026 SITE 2 BC1 5 HOH B2027 SITE 1 BC2 6 DC B 106 HOH B2006 HOH B2025 DC C 209 SITE 2 BC2 6 DC C 210 HOH C2011 CRYST1 65.614 100.543 204.341 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 0.015241 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009946 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004894 0.00000