HEADER TRANSFERASE/DNA 01-OCT-13 4C8M TITLE BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS TITLE 2 AQUATICUS WITH THE ARITIFICIAL BASE PAIR D5SICS-DNAM AT THE TITLE 3 POSTINSERTION SITE (SEQUENCE CONTEXT 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LARGE FRAGMENT OF TAQ DNA POLYMERASE I; 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 MOL_ID: 2; COMPND 8 MOLECULE: PRIMER, 5'-D(*GP*CP*CP*AP*CP*GP*GP*CP*GP*CP*BMNP)-3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: TEMPLATE, 5'-D(*TP*TP*CP* COMPND 13 LHOP*GP*CP*GP*CP*CP*GP*TP*GP*GP*CP)-3'; COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 7 ORGANISM_TAXID: 32630; SOURCE 8 MOL_ID: 3; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS TRANSFERASE-DNA COMPLEX, UNNATURAL BASE PAIR 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 08-MAY-24 4C8M 1 REMARK LINK REVDAT 3 23-AUG-17 4C8M 1 REMARK REVDAT 2 25-DEC-13 4C8M 1 JRNL HETATM REVDAT 1 11-DEC-13 4C8M 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. 1.57 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 21.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 94768 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 9061 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 49.2607 - 4.8720 1.00 5825 313 0.1380 0.1533 REMARK 3 2 4.8720 - 3.8675 1.00 5837 307 0.1317 0.1551 REMARK 3 3 3.8675 - 3.3788 1.00 5806 292 0.1612 0.1824 REMARK 3 4 3.3788 - 3.0699 1.00 5850 313 0.1832 0.2388 REMARK 3 5 3.0699 - 2.8499 1.00 5804 321 0.1829 0.2040 REMARK 3 6 2.8499 - 2.6819 1.00 5748 401 0.1737 0.2018 REMARK 3 7 2.6819 - 2.5476 1.00 5845 276 0.1694 0.2101 REMARK 3 8 2.5476 - 2.4367 1.00 5859 281 0.1605 0.1732 REMARK 3 9 2.4367 - 2.3429 1.00 5833 266 0.1553 0.1876 REMARK 3 10 2.3429 - 2.2620 1.00 5825 324 0.1598 0.1994 REMARK 3 11 2.2620 - 2.1913 1.00 5841 341 0.1720 0.2397 REMARK 3 12 2.1913 - 2.1287 1.00 5796 311 0.1787 0.2279 REMARK 3 13 2.1287 - 2.0726 1.00 5800 265 0.1848 0.2561 REMARK 3 14 2.0726 - 2.0220 1.00 5857 308 0.1956 0.2469 REMARK 3 15 2.0220 - 1.9761 1.00 5873 278 0.1959 0.2254 REMARK 3 16 1.9761 - 1.9340 1.00 5804 311 0.2060 0.2734 REMARK 3 17 1.9340 - 1.8953 1.00 5790 353 0.2281 0.2737 REMARK 3 18 1.8953 - 1.8596 1.00 5849 284 0.2401 0.2931 REMARK 3 19 1.8596 - 1.8264 1.00 5809 270 0.2620 0.3083 REMARK 3 20 1.8264 - 1.7954 1.00 5891 342 0.2944 0.3192 REMARK 3 21 1.7954 - 1.7664 1.00 5700 332 0.3227 0.3554 REMARK 3 22 1.7664 - 1.7393 1.00 5873 309 0.3254 0.3519 REMARK 3 23 1.7393 - 1.7137 1.00 5807 296 0.3420 0.3592 REMARK 3 24 1.7137 - 1.6895 1.00 5819 297 0.3434 0.3303 REMARK 3 25 1.6895 - 1.6667 0.99 5791 289 0.3612 0.3786 REMARK 3 26 1.6667 - 1.6451 0.99 5764 305 0.3856 0.3766 REMARK 3 27 1.6451 - 1.6245 0.98 5740 248 0.4271 0.4337 REMARK 3 28 1.6245 - 1.6049 0.96 5595 303 0.4498 0.4004 REMARK 3 29 1.6049 - 1.5863 0.93 5360 255 0.4686 0.4516 REMARK 3 30 1.5863 - 1.5684 0.79 4670 270 0.4842 0.4892 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) : 30.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.22 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 5038 REMARK 3 ANGLE : 1.283 6941 REMARK 3 CHIRALITY : 0.055 755 REMARK 3 PLANARITY : 0.008 848 REMARK 3 DIHEDRAL : 16.907 1980 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): -23.0276 -31.9710 27.3351 REMARK 3 T TENSOR REMARK 3 T11: 0.2673 T22: 0.4781 REMARK 3 T33: 0.2705 T12: 0.0145 REMARK 3 T13: 0.0109 T23: 0.0420 REMARK 3 L TENSOR REMARK 3 L11: 2.2951 L22: 0.7872 REMARK 3 L33: 1.4979 L12: -0.4507 REMARK 3 L13: 0.1858 L23: -0.3122 REMARK 3 S TENSOR REMARK 3 S11: -0.1107 S12: -0.3648 S13: -0.0842 REMARK 3 S21: 0.1459 S22: 0.1588 S23: 0.1996 REMARK 3 S31: -0.0678 S32: -0.7287 S33: -0.0510 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 453 THROUGH 603 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.1713 -22.4050 39.6505 REMARK 3 T TENSOR REMARK 3 T11: 0.3010 T22: 0.3553 REMARK 3 T33: 0.2877 T12: 0.0208 REMARK 3 T13: 0.0225 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 1.4093 L22: 1.7411 REMARK 3 L33: 1.7954 L12: 0.6091 REMARK 3 L13: 0.4092 L23: 0.5556 REMARK 3 S TENSOR REMARK 3 S11: 0.0261 S12: 0.0253 S13: 0.1104 REMARK 3 S21: 0.0863 S22: 0.1087 S23: -0.2074 REMARK 3 S31: -0.1411 S32: 0.3021 S33: -0.1453 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 604 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.9771 -32.3295 14.3332 REMARK 3 T TENSOR REMARK 3 T11: 0.2503 T22: 0.2671 REMARK 3 T33: 0.2674 T12: 0.0123 REMARK 3 T13: -0.0038 T23: 0.0048 REMARK 3 L TENSOR REMARK 3 L11: 1.0354 L22: 0.4666 REMARK 3 L33: 1.3579 L12: 0.3036 REMARK 3 L13: -0.0942 L23: -0.3527 REMARK 3 S TENSOR REMARK 3 S11: -0.0246 S12: 0.1096 S13: 0.0271 REMARK 3 S21: -0.0049 S22: -0.0274 S23: -0.0788 REMARK 3 S31: 0.0520 S32: 0.1666 S33: 0.0667 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND (RESID 102 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.3414 -14.5805 35.2644 REMARK 3 T TENSOR REMARK 3 T11: 0.4323 T22: 0.3488 REMARK 3 T33: 0.3469 T12: -0.0500 REMARK 3 T13: -0.0515 T23: -0.0579 REMARK 3 L TENSOR REMARK 3 L11: 4.7971 L22: 0.8917 REMARK 3 L33: 3.9560 L12: -0.3838 REMARK 3 L13: -1.7420 L23: -1.1332 REMARK 3 S TENSOR REMARK 3 S11: -0.0691 S12: 1.0904 S13: -0.1697 REMARK 3 S21: -0.1220 S22: -0.0580 S23: 0.0776 REMARK 3 S31: 0.0545 S32: -0.5165 S33: 0.1094 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN C AND (RESID 204 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.3530 -14.1078 35.1676 REMARK 3 T TENSOR REMARK 3 T11: 0.5555 T22: 0.4492 REMARK 3 T33: 0.4438 T12: -0.0128 REMARK 3 T13: 0.0256 T23: 0.0239 REMARK 3 L TENSOR REMARK 3 L11: 5.4017 L22: 4.9487 REMARK 3 L33: 4.9411 L12: -3.9860 REMARK 3 L13: -3.8490 L23: 4.9869 REMARK 3 S TENSOR REMARK 3 S11: 0.2850 S12: 1.0465 S13: 0.1101 REMARK 3 S21: -0.5446 S22: -0.1078 S23: -0.0753 REMARK 3 S31: -0.3987 S32: -0.6967 S33: -0.1472 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 4C8M 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_1290058488. 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 : 94841 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 49.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.780 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 (%): 50.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 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 102.27150 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 102.27150 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 32.68700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.72800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.68700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.72800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 102.27150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.68700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.72800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 102.27150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.68700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.72800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.9 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 C2009 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 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 204 O4' - C1' - N1 ANGL. DEV. = 2.8 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 381 111.99 -168.78 REMARK 500 THR A 399 -168.61 -106.66 REMARK 500 ILE A 503 -79.02 -72.55 REMARK 500 THR A 588 139.19 66.50 REMARK 500 ARG A 636 -162.54 -102.07 REMARK 500 HIS A 784 -120.91 48.88 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 B2113 O REMARK 620 2 HOH B2114 O 179.0 REMARK 620 3 HOH B2115 O 89.4 91.5 REMARK 620 4 HOH B2116 O 91.7 88.1 88.8 REMARK 620 5 HOH B2117 O 89.3 91.0 89.3 177.8 REMARK 620 6 HOH B2118 O 88.6 90.5 177.9 90.5 91.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C1216 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C2216 O REMARK 620 2 HOH C2217 O 179.3 REMARK 620 3 HOH C2218 O 89.7 90.4 REMARK 620 4 HOH C2219 O 88.4 92.2 91.4 REMARK 620 5 HOH C2220 O 90.4 88.9 89.5 178.5 REMARK 620 6 HOH C2221 O 88.1 91.7 177.6 89.6 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 MG C 1216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 1217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1112 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1836 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1837 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1838 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1839 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: 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'-T OF THE TEMPLATE IS NOT RESOLVED IN THE STRUCTURE DBREF 4C8M A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4C8M B 102 112 PDB 4C8M 4C8M 102 112 DBREF 4C8M C 202 215 PDB 4C8M 4C8M 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 BMN SEQRES 1 C 14 DT DT DC LHO DG DC DG DC DC DG DT DG DG SEQRES 2 C 14 DC HET BMN B 112 40 HET LHO C 205 38 HET SO4 A1833 5 HET SO4 A1834 5 HET GOL A1835 14 HET SO4 A1836 5 HET GOL A1837 14 HET GOL A1838 14 HET GOL A1839 14 HET MG B1112 1 HET MG C1216 1 HET GOL C1217 14 HETNAM BMN (1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)- HETNAM 2 BMN 5-O-PHOSPHONO-D-ERYTHRO-PENTITOL HETNAM LHO 2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 LHO PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 BMN C16 H19 O7 P FORMUL 3 LHO C15 H18 N O6 P S FORMUL 4 SO4 3(O4 S 2-) FORMUL 6 GOL 5(C3 H8 O3) FORMUL 11 MG 2(MG 2+) FORMUL 14 HOH *350(H2 O) HELIX 1 1 GLU A 315 ALA A 319 5 5 HELIX 2 2 GLU A 337 LEU A 342 1 6 HELIX 3 3 ARG A 343 LEU A 345 5 3 HELIX 4 4 LEU A 352 GLU A 363 1 12 HELIX 5 5 ASP A 372 ASP A 381 1 10 HELIX 6 6 THR A 386 GLY A 395 1 10 HELIX 7 7 GLU A 401 LEU A 420 1 20 HELIX 8 8 GLU A 423 VAL A 433 1 11 HELIX 9 9 VAL A 433 GLY A 448 1 16 HELIX 10 10 ASP A 452 GLY A 479 1 28 HELIX 11 11 SER A 486 ASP A 496 1 11 HELIX 12 12 SER A 515 ALA A 521 1 7 HELIX 13 13 HIS A 526 ILE A 546 1 21 HELIX 14 14 LEU A 549 LEU A 552 5 4 HELIX 15 15 ASN A 580 ILE A 584 5 5 HELIX 16 16 ARG A 587 ARG A 596 1 10 HELIX 17 17 GLN A 613 GLY A 624 1 12 HELIX 18 18 ASP A 625 GLY A 635 1 11 HELIX 19 19 ASP A 637 GLY A 648 1 12 HELIX 20 20 PRO A 650 VAL A 654 5 5 HELIX 21 21 ASP A 655 VAL A 669 1 15 HELIX 22 22 SER A 674 ALA A 683 1 10 HELIX 23 23 PRO A 685 PHE A 700 1 16 HELIX 24 24 PHE A 700 GLY A 718 1 19 HELIX 25 25 PRO A 731 ALA A 735 5 5 HELIX 26 26 VAL A 737 GLU A 774 1 38 HELIX 27 27 LYS A 793 GLY A 809 1 17 HELIX 28 28 ASP A 826 LYS A 831 1 6 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 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 BMN B 112 1555 1555 1.60 LINK O3' DC C 204 P LHO C 205 1555 1555 1.61 LINK O3' LHO C 205 P DG C 206 1555 1555 1.61 LINK MG MG B1112 O HOH B2113 1555 1555 2.18 LINK MG MG B1112 O HOH B2114 1555 1555 2.19 LINK MG MG B1112 O HOH B2115 1555 1555 2.17 LINK MG MG B1112 O HOH B2116 1555 1555 2.18 LINK MG MG B1112 O HOH B2117 1555 1555 2.18 LINK MG MG B1112 O HOH B2118 1555 1555 2.18 LINK MG MG C1216 O HOH C2216 1555 1555 2.18 LINK MG MG C1216 O HOH C2217 1555 1555 2.20 LINK MG MG C1216 O HOH C2218 1555 1555 2.18 LINK MG MG C1216 O HOH C2219 1555 1555 2.19 LINK MG MG C1216 O HOH C2220 1555 1555 2.18 LINK MG MG C1216 O HOH C2221 1555 1555 2.17 CISPEP 1 TRP A 299 PRO A 300 0 2.74 CISPEP 2 ASP A 578 PRO A 579 0 0.92 SITE 1 AC1 6 HOH C2216 HOH C2217 HOH C2218 HOH C2219 SITE 2 AC1 6 HOH C2220 HOH C2221 SITE 1 AC2 4 DC B 106 HOH B2113 DC C 209 DC C 210 SITE 1 AC3 5 SER A 674 ALA A 675 HIS A 676 TYR A 686 SITE 2 AC3 5 HOH A2262 SITE 1 AC4 3 ARG A 393 ARG A 419 HOH A2050 SITE 1 AC5 6 HOH B2113 HOH B2114 HOH B2115 HOH B2116 SITE 2 AC5 6 HOH B2117 HOH B2118 SITE 1 AC6 4 ARG A 411 ASN A 415 HOH A2053 HOH A2317 SITE 1 AC7 2 ARG A 431 ARG A 435 SITE 1 AC8 6 MET A 317 TRP A 318 ALA A 319 ASP A 320 SITE 2 AC8 6 GLU A 465 HIS A 554 SITE 1 AC9 5 GLN A 613 HIS A 639 ARG A 659 LYS A 663 SITE 2 AC9 5 HOH A2215 SITE 1 BC1 4 TRP A 428 TYR A 811 HOH A2084 HOH A2318 CRYST1 65.374 101.456 204.543 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 0.015297 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004889 0.00000