HEADER TRANSFERASE/DNA 19-MAR-10 3M8S TITLE CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM TITLE 2 THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH TRAPPED 4'- TITLE 3 METHYLATED DTTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KLENOW FRAGMENT; COMPND 5 SYNONYM: TAQ POLYMERASE 1; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- COMPND 14 3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POLA, POL1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS DNA, DNA POLYMERASE, DNA REPLICATION, NUCLEOTIDES, MODIFIED KEYWDS 2 NUCLEOTIDE, ARTIFICIAL NUCLEOTIDE, NUCLEOTIDE PROBES, DNA-BINDING, KEYWDS 3 DNA-DIRECTED DNA POLYMERASE, NUCLEOTIDYLTRANSFERASE, TRANSFERASE, KEYWDS 4 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.DIEDERICHS,A.MARX,K.BETZ REVDAT 3 06-SEP-23 3M8S 1 REMARK LINK REVDAT 2 08-SEP-10 3M8S 1 JRNL REVDAT 1 07-JUL-10 3M8S 0 JRNL AUTH K.BETZ,F.STRECKENBACH,A.SCHNUR,T.EXNER,W.WELTE,K.DIEDERICHS, JRNL AUTH 2 A.MARX JRNL TITL STRUCTURES OF DNA POLYMERASES CAUGHT PROCESSING JRNL TITL 2 SIZE-AUGMENTED NUCLEOTIDE PROBES. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 49 5181 2010 JRNL REFN ISSN 1433-7851 JRNL PMID 20572212 JRNL DOI 10.1002/ANIE.200905724 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6_289) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 31860 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1600 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 47.1035 - 4.8912 1.00 2885 163 0.1571 0.1897 REMARK 3 2 4.8912 - 3.8829 1.00 2786 152 0.1281 0.1645 REMARK 3 3 3.8829 - 3.3922 1.00 2741 161 0.1457 0.1950 REMARK 3 4 3.3922 - 3.0821 1.00 2749 148 0.1707 0.2329 REMARK 3 5 3.0821 - 2.8612 1.00 2738 141 0.1812 0.2524 REMARK 3 6 2.8612 - 2.6926 1.00 2729 145 0.1906 0.2582 REMARK 3 7 2.6926 - 2.5577 1.00 2727 154 0.1871 0.2625 REMARK 3 8 2.5577 - 2.4464 1.00 2730 149 0.1860 0.2457 REMARK 3 9 2.4464 - 2.3522 1.00 2714 119 0.1994 0.2629 REMARK 3 10 2.3522 - 2.2711 1.00 2724 141 0.2269 0.3068 REMARK 3 11 2.2711 - 2.2000 1.00 2737 127 0.2575 0.3618 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 : 0.39 REMARK 3 B_SOL : 32.40 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 5095 REMARK 3 ANGLE : 0.970 6990 REMARK 3 CHIRALITY : 0.062 760 REMARK 3 PLANARITY : 0.003 809 REMARK 3 DIHEDRAL : 19.360 1982 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 294:418) REMARK 3 ORIGIN FOR THE GROUP (A): 42.4741 -42.9782 -17.5253 REMARK 3 T TENSOR REMARK 3 T11: 0.3721 T22: 0.1974 REMARK 3 T33: 0.3326 T12: -0.0386 REMARK 3 T13: 0.0971 T23: -0.0248 REMARK 3 L TENSOR REMARK 3 L11: 0.4750 L22: 0.2042 REMARK 3 L33: 0.6366 L12: -0.1768 REMARK 3 L13: -0.0071 L23: 0.0200 REMARK 3 S TENSOR REMARK 3 S11: -0.0849 S12: 0.0634 S13: -0.0730 REMARK 3 S21: -0.1912 S22: 0.0482 S23: -0.1973 REMARK 3 S31: 0.3231 S32: 0.0214 S33: 0.0536 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 419:600) REMARK 3 ORIGIN FOR THE GROUP (A): 34.5345 -15.5931 -2.1522 REMARK 3 T TENSOR REMARK 3 T11: 0.2212 T22: 0.1871 REMARK 3 T33: 0.1743 T12: -0.0462 REMARK 3 T13: 0.0205 T23: -0.0160 REMARK 3 L TENSOR REMARK 3 L11: 0.5602 L22: 0.9313 REMARK 3 L33: 0.8871 L12: 0.4198 REMARK 3 L13: -0.0232 L23: 0.0804 REMARK 3 S TENSOR REMARK 3 S11: 0.0282 S12: -0.0377 S13: 0.0355 REMARK 3 S21: -0.0171 S22: -0.0440 S23: -0.0119 REMARK 3 S31: -0.1611 S32: -0.0571 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 601:693) REMARK 3 ORIGIN FOR THE GROUP (A): 12.2010 -13.3695 -7.6607 REMARK 3 T TENSOR REMARK 3 T11: 0.3125 T22: 0.4445 REMARK 3 T33: 0.1732 T12: 0.0956 REMARK 3 T13: 0.0244 T23: 0.0537 REMARK 3 L TENSOR REMARK 3 L11: 0.2907 L22: 0.3045 REMARK 3 L33: 0.6664 L12: 0.0326 REMARK 3 L13: 0.4335 L23: -0.0330 REMARK 3 S TENSOR REMARK 3 S11: -0.0797 S12: -0.1372 S13: 0.0642 REMARK 3 S21: 0.0938 S22: 0.0964 S23: 0.0992 REMARK 3 S31: -0.3650 S32: -0.3255 S33: -0.0092 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 694:786) REMARK 3 ORIGIN FOR THE GROUP (A): 15.8338 -30.1407 -9.2582 REMARK 3 T TENSOR REMARK 3 T11: 0.2234 T22: 0.3427 REMARK 3 T33: 0.1821 T12: -0.0559 REMARK 3 T13: 0.0126 T23: 0.0259 REMARK 3 L TENSOR REMARK 3 L11: 0.6040 L22: 0.4369 REMARK 3 L33: 0.7206 L12: 0.0310 REMARK 3 L13: 0.5984 L23: -0.0043 REMARK 3 S TENSOR REMARK 3 S11: -0.0623 S12: 0.0411 S13: -0.0273 REMARK 3 S21: -0.1516 S22: 0.1640 S23: 0.0532 REMARK 3 S31: 0.0101 S32: -0.4537 S33: -0.1013 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 787:832) REMARK 3 ORIGIN FOR THE GROUP (A): 23.2255 -15.1082 -25.7853 REMARK 3 T TENSOR REMARK 3 T11: 0.4479 T22: 0.3856 REMARK 3 T33: 0.1750 T12: -0.0092 REMARK 3 T13: -0.0467 T23: 0.0671 REMARK 3 L TENSOR REMARK 3 L11: 0.4341 L22: 0.3443 REMARK 3 L33: 1.2810 L12: 0.0963 REMARK 3 L13: -0.5474 L23: 0.3198 REMARK 3 S TENSOR REMARK 3 S11: -0.0448 S12: 0.3341 S13: 0.0036 REMARK 3 S21: -0.2738 S22: 0.1326 S23: -0.0504 REMARK 3 S31: -0.6458 S32: -0.4959 S33: -0.0726 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B) REMARK 3 ORIGIN FOR THE GROUP (A): 34.7217 -22.1872 2.5256 REMARK 3 T TENSOR REMARK 3 T11: 0.1524 T22: 0.2507 REMARK 3 T33: 0.2259 T12: -0.0207 REMARK 3 T13: -0.0255 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 0.1200 L22: 1.5288 REMARK 3 L33: 2.5003 L12: -0.4036 REMARK 3 L13: 0.0408 L23: -0.8583 REMARK 3 S TENSOR REMARK 3 S11: -0.0759 S12: 0.1722 S13: -0.0337 REMARK 3 S21: 0.0993 S22: -0.0163 S23: -0.1712 REMARK 3 S31: -0.2796 S32: 0.2925 S33: 0.0586 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN C) REMARK 3 ORIGIN FOR THE GROUP (A): 32.7826 -23.0454 6.3551 REMARK 3 T TENSOR REMARK 3 T11: 0.1867 T22: 0.3044 REMARK 3 T33: 0.1826 T12: 0.0104 REMARK 3 T13: -0.0184 T23: 0.0315 REMARK 3 L TENSOR REMARK 3 L11: 0.6588 L22: 0.4275 REMARK 3 L33: 1.2802 L12: 0.0326 REMARK 3 L13: 0.7703 L23: 0.0592 REMARK 3 S TENSOR REMARK 3 S11: -0.2001 S12: -0.3096 S13: -0.1535 REMARK 3 S21: 0.0155 S22: 0.0938 S23: -0.0416 REMARK 3 S31: 0.1307 S32: -0.2920 S33: 0.0835 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 3M8S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000058251. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-09 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) : 1.0000 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT. SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : THIS NOISE-FREE COUNTING DEVICE REMARK 200 COMBINES EXTRAORDINARY SPATIAL REMARK 200 RESOLUTION WITH FULL FRAME READ- REMARK 200 OUT TIMES OF 5 MS. THESE REMARK 200 FEATURES MAKE IT AN IDEAL REMARK 200 DETECTOR FOR PX AND ENABLE NOVEL REMARK 200 DATA ACQUISITION MODES SUCH AS REMARK 200 CONTINUOS DATA ACQUISITION AND REMARK 200 FINE-PHI-SLICING. REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32046 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 47.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.760 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 9.25 REMARK 200 R MERGE FOR SHELL (I) : 0.01052 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.940 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 3KTQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG 8000, 0.2M AMMONIUM REMARK 280 ACETATE, 0.02M MAGNESIUM ACETATE, 0.05M SODIUM CACODYLATE, PH REMARK 280 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 30.25167 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 60.50333 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 60.50333 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 30.25167 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: 7760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 293 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 832 CG CD OE1 OE2 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 101 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA B 105 O3' - P - O5' ANGL. DEV. = -16.1 DEGREES REMARK 500 DA B 105 O3' - P - OP2 ANGL. DEV. = -22.4 DEGREES REMARK 500 DA B 105 O3' - P - OP1 ANGL. DEV. = -26.7 DEGREES REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 2.1 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 381 107.48 -167.96 REMARK 500 VAL A 433 -72.89 -123.73 REMARK 500 HIS A 480 154.74 179.65 REMARK 500 HIS A 526 140.10 -173.01 REMARK 500 TYR A 545 -59.55 -126.81 REMARK 500 VAL A 586 -15.49 -156.90 REMARK 500 GLN A 613 48.21 36.66 REMARK 500 HIS A 784 -78.51 73.60 REMARK 500 TYR A 811 93.90 -171.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 15P A 835 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 A 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 68 O REMARK 620 2 HXB A 113 O10 85.0 REMARK 620 3 ASP A 610 OD2 83.5 95.4 REMARK 620 4 ASP A 785 OD1 164.3 87.2 110.8 REMARK 620 5 HOH A 840 O 87.3 160.7 101.3 95.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 2 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HXB A 113 O6 REMARK 620 2 HXB A 113 O10 88.9 REMARK 620 3 HXB A 113 O9 87.6 77.8 REMARK 620 4 ASP A 610 OD1 100.4 102.8 172.0 REMARK 620 5 TYR A 611 O 94.7 172.2 95.4 83.4 REMARK 620 6 ASP A 785 OD2 175.3 87.4 88.8 83.2 88.7 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 HXB A 113 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 15P A 835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 836 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 837 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KTQ RELATED DB: PDB REMARK 900 RELATED ID: 1QTM RELATED DB: PDB REMARK 900 RELATED ID: 3M8R RELATED DB: PDB DBREF 3M8S A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 3M8S B 101 112 PDB 3M8S 3M8S 101 112 DBREF 3M8S C 201 216 PDB 3M8S 3M8S 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 DA DA DG DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC MODRES 3M8S DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC B 112 18 HET HXB A 113 30 HET MG A 1 1 HET MG A 2 1 HET GOL A 833 6 HET PEG A 834 7 HET 15P A 835 10 HET ACT A 836 4 HET ACT A 837 4 HET ACT A 3 4 HET GOL B 3 6 HET GOL C 1 6 HET ACT C 4 4 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM HXB 4'-METHYLTHYMIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE) HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM 15P POLYETHYLENE GLYCOL (N=34) HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 15P PEG 1500 FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 HXB C11 H19 N2 O14 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 GOL 3(C3 H8 O3) FORMUL 8 PEG C4 H10 O3 FORMUL 9 15P C69 H140 O35 FORMUL 10 ACT 4(C2 H3 O2 1-) FORMUL 16 HOH *122(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 TYR A 545 1 20 HELIX 13 13 PRO A 548 ILE A 553 5 6 HELIX 14 14 THR A 588 ARG A 596 1 9 HELIX 15 15 GLN A 613 GLY A 624 1 12 HELIX 16 16 ASP A 625 GLU A 634 1 10 HELIX 17 17 ASP A 637 PHE A 647 1 11 HELIX 18 18 PRO A 650 VAL A 654 5 5 HELIX 19 19 ASP A 655 TYR A 671 1 17 HELIX 20 20 SER A 674 ALA A 683 1 10 HELIX 21 21 PRO A 685 SER A 699 1 15 HELIX 22 22 PRO A 701 GLY A 718 1 18 HELIX 23 23 PRO A 731 ALA A 735 5 5 HELIX 24 24 VAL A 737 MET A 775 1 39 HELIX 25 25 ARG A 795 GLY A 809 1 15 HELIX 26 26 ASP A 826 GLU A 832 1 7 SHEET 1 A 4 GLU A 295 GLU A 296 0 SHEET 2 A 4 ARG A 331 ARG A 334 1 O VAL A 332 N GLU A 295 SHEET 3 A 4 LEU A 321 ALA A 327 -1 N ALA A 326 O HIS A 333 SHEET 4 A 4 PHE A 306 LEU A 311 -1 N GLY A 308 O ALA A 325 SHEET 1 B 2 ARG A 450 LEU A 451 0 SHEET 2 B 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 C 2 ARG A 563 ASN A 565 0 SHEET 2 C 2 SER A 575 SER A 577 -1 O SER A 577 N ARG A 563 SHEET 1 D 4 ARG A 778 GLN A 782 0 SHEET 2 D 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 D 4 TRP A 604 TYR A 611 -1 N VAL A 607 O LEU A 789 SHEET 4 D 4 VAL A 819 GLY A 824 -1 O GLY A 824 N LEU A 606 SHEET 1 E 2 TYR A 719 GLU A 721 0 SHEET 2 E 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK O3' DC B 111 P DOC B 112 1555 1555 1.60 LINK MG MG A 1 O HOH A 68 1555 1555 2.63 LINK MG MG A 1 O10 HXB A 113 1555 1555 2.54 LINK MG MG A 1 OD2 ASP A 610 1555 1555 2.42 LINK MG MG A 1 OD1 ASP A 785 1555 1555 2.08 LINK MG MG A 1 O HOH A 840 1555 1555 2.41 LINK MG MG A 2 O6 HXB A 113 1555 1555 1.85 LINK MG MG A 2 O10 HXB A 113 1555 1555 2.11 LINK MG MG A 2 O9 HXB A 113 1555 1555 2.14 LINK MG MG A 2 OD1 ASP A 610 1555 1555 2.06 LINK MG MG A 2 O TYR A 611 1555 1555 2.01 LINK MG MG A 2 OD2 ASP A 785 1555 1555 2.08 CISPEP 1 TRP A 299 PRO A 300 0 2.62 CISPEP 2 ASP A 578 PRO A 579 0 -0.86 SITE 1 AC1 22 MG A 1 MG A 2 HOH A 36 HOH A 68 SITE 2 AC1 22 HOH A 77 HOH A 111 ARG A 573 ASP A 610 SITE 3 AC1 22 TYR A 611 SER A 612 GLN A 613 ILE A 614 SITE 4 AC1 22 GLU A 615 HIS A 639 ARG A 659 LYS A 663 SITE 5 AC1 22 THR A 664 PHE A 667 ASP A 785 DOC B 112 SITE 6 AC1 22 DA C 204 DG C 205 SITE 1 AC2 7 MG A 2 HOH A 68 HXB A 113 ASP A 610 SITE 2 AC2 7 ASP A 785 HOH A 840 DOC B 112 SITE 1 AC3 5 MG A 1 HXB A 113 ASP A 610 TYR A 611 SITE 2 AC3 5 ASP A 785 SITE 1 AC4 3 GLY A 672 ARG A 746 DA C 203 SITE 1 AC5 5 ARG A 425 TRP A 428 LEU A 723 PHE A 724 SITE 2 AC5 5 TYR A 811 SITE 1 AC6 7 THR A 544 PRO A 579 ASN A 580 ASN A 583 SITE 2 AC6 7 HOH C 88 DC C 209 DC C 210 SITE 1 AC7 3 ARG A 313 TRP A 318 LEU A 552 SITE 1 AC8 4 ASP A 452 TYR A 455 ARG A 596 ILE A 599 SITE 1 AC9 4 ARG A 728 TYR A 729 VAL A 730 ACT C 4 SITE 1 BC1 2 DG B 107 DG B 108 SITE 1 BC2 4 HOH C 31 DG C 205 DG C 206 DC C 207 SITE 1 BC3 4 ACT A 3 ARG A 728 DG C 206 DC C 207 CRYST1 108.742 108.742 90.755 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 0.009196 0.005309 0.000000 0.00000 SCALE2 0.000000 0.010619 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011019 0.00000