PDB Short entry for 3M8R HEADER TRANSFERASE/DNA 19-MAR-10 3M8R 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 ETHYLATED 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 3M8R 1 REMARK LINK REVDAT 2 08-SEP-10 3M8R 1 JRNL REVDAT 1 07-JUL-10 3M8R 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 42156 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 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 : 2108 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 47.1201 - 4.9307 1.00 2815 161 0.1722 0.1955 REMARK 3 2 4.9307 - 3.9142 1.00 2708 141 0.1393 0.1719 REMARK 3 3 3.9142 - 3.4196 1.00 2679 159 0.1527 0.1812 REMARK 3 4 3.4196 - 3.1070 1.00 2663 149 0.1821 0.2043 REMARK 3 5 3.1070 - 2.8844 1.00 2690 137 0.1942 0.2360 REMARK 3 6 2.8844 - 2.7143 1.00 2655 138 0.1931 0.2140 REMARK 3 7 2.7143 - 2.5784 1.00 2632 149 0.1867 0.2562 REMARK 3 8 2.5784 - 2.4662 1.00 2656 149 0.1881 0.2518 REMARK 3 9 2.4662 - 2.3712 1.00 2670 125 0.1855 0.2536 REMARK 3 10 2.3712 - 2.2894 1.00 2663 123 0.1954 0.2646 REMARK 3 11 2.2894 - 2.2178 1.00 2618 143 0.1973 0.2696 REMARK 3 12 2.2178 - 2.1544 1.00 2684 127 0.2033 0.2632 REMARK 3 13 2.1544 - 2.0977 1.00 2657 126 0.2061 0.2633 REMARK 3 14 2.0977 - 2.0465 1.00 2587 149 0.2094 0.2711 REMARK 3 15 2.0465 - 2.0000 1.00 2671 132 0.2159 0.2799 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 : 0.38 REMARK 3 B_SOL : 41.43 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.52 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 5095 REMARK 3 ANGLE : 0.827 6990 REMARK 3 CHIRALITY : 0.045 760 REMARK 3 PLANARITY : 0.003 806 REMARK 3 DIHEDRAL : 18.395 1990 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 294:419) REMARK 3 ORIGIN FOR THE GROUP (A): 42.3739 -43.0123 -17.4846 REMARK 3 T TENSOR REMARK 3 T11: 0.2936 T22: 0.1515 REMARK 3 T33: 0.3167 T12: -0.0479 REMARK 3 T13: 0.0649 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 1.8357 L22: 0.4745 REMARK 3 L33: 1.4930 L12: 0.2153 REMARK 3 L13: -0.2736 L23: 0.1741 REMARK 3 S TENSOR REMARK 3 S11: 0.0046 S12: -0.0029 S13: -0.3176 REMARK 3 S21: -0.1441 S22: 0.0429 S23: -0.2929 REMARK 3 S31: 0.4578 S32: 0.0647 S33: -0.0247 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 420:523) REMARK 3 ORIGIN FOR THE GROUP (A): 33.4766 -16.3535 1.1684 REMARK 3 T TENSOR REMARK 3 T11: 0.1557 T22: 0.1470 REMARK 3 T33: 0.1785 T12: 0.0037 REMARK 3 T13: 0.0124 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 0.8799 L22: 1.6693 REMARK 3 L33: 1.5143 L12: 0.8684 REMARK 3 L13: -0.3567 L23: -0.2028 REMARK 3 S TENSOR REMARK 3 S11: 0.1246 S12: -0.0493 S13: 0.1048 REMARK 3 S21: 0.0928 S22: -0.1020 S23: 0.1074 REMARK 3 S31: -0.3796 S32: -0.0726 S33: -0.0399 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 524:631) REMARK 3 ORIGIN FOR THE GROUP (A): 30.0394 -15.2837 -9.7376 REMARK 3 T TENSOR REMARK 3 T11: 0.1767 T22: 0.1848 REMARK 3 T33: 0.1474 T12: 0.0221 REMARK 3 T13: 0.0272 T23: 0.0098 REMARK 3 L TENSOR REMARK 3 L11: 0.4897 L22: 0.5497 REMARK 3 L33: 2.5133 L12: 0.8544 REMARK 3 L13: -0.0770 L23: -0.5243 REMARK 3 S TENSOR REMARK 3 S11: -0.0579 S12: 0.0703 S13: 0.0443 REMARK 3 S21: -0.0375 S22: 0.1115 S23: 0.0309 REMARK 3 S31: -0.3786 S32: -0.4291 S33: -0.0860 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 632:729) REMARK 3 ORIGIN FOR THE GROUP (A): 9.7353 -19.1361 -3.6197 REMARK 3 T TENSOR REMARK 3 T11: 0.2684 T22: 0.9627 REMARK 3 T33: 0.2788 T12: 0.1759 REMARK 3 T13: 0.0574 T23: 0.1697 REMARK 3 L TENSOR REMARK 3 L11: 0.4231 L22: 0.8517 REMARK 3 L33: 2.3388 L12: -0.0184 REMARK 3 L13: -0.0881 L23: -0.5078 REMARK 3 S TENSOR REMARK 3 S11: -0.0498 S12: -0.1371 S13: 0.0670 REMARK 3 S21: 0.1069 S22: 0.4162 S23: 0.2127 REMARK 3 S31: -0.4222 S32: -1.3918 S33: -0.3256 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 730:832) REMARK 3 ORIGIN FOR THE GROUP (A): 22.1560 -22.8208 -17.9673 REMARK 3 T TENSOR REMARK 3 T11: 0.2342 T22: 0.3988 REMARK 3 T33: 0.1735 T12: -0.0333 REMARK 3 T13: -0.0068 T23: 0.0503 REMARK 3 L TENSOR REMARK 3 L11: 0.6992 L22: 0.4641 REMARK 3 L33: 1.1868 L12: 0.0206 REMARK 3 L13: -0.0362 L23: 0.2490 REMARK 3 S TENSOR REMARK 3 S11: -0.1175 S12: 0.1038 S13: -0.0239 REMARK 3 S21: -0.2128 S22: 0.1845 S23: 0.0495 REMARK 3 S31: -0.1507 S32: -0.5569 S33: -0.0991 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B) REMARK 3 ORIGIN FOR THE GROUP (A): 34.5191 -22.2118 2.4158 REMARK 3 T TENSOR REMARK 3 T11: 0.1106 T22: 0.1979 REMARK 3 T33: 0.2176 T12: -0.0009 REMARK 3 T13: -0.0244 T23: 0.0227 REMARK 3 L TENSOR REMARK 3 L11: 0.3482 L22: 1.2783 REMARK 3 L33: 3.2491 L12: 0.3239 REMARK 3 L13: -1.0937 L23: -0.9658 REMARK 3 S TENSOR REMARK 3 S11: 0.0154 S12: 0.0456 S13: -0.1201 REMARK 3 S21: 0.0430 S22: -0.0162 S23: -0.0986 REMARK 3 S31: -0.1830 S32: 0.0381 S33: -0.0025 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN C) REMARK 3 ORIGIN FOR THE GROUP (A): 32.6210 -23.0437 6.3132 REMARK 3 T TENSOR REMARK 3 T11: 0.1064 T22: 0.2205 REMARK 3 T33: 0.1429 T12: 0.0498 REMARK 3 T13: -0.0115 T23: 0.0621 REMARK 3 L TENSOR REMARK 3 L11: 0.3424 L22: 0.6121 REMARK 3 L33: 2.8140 L12: 0.4303 REMARK 3 L13: 0.2766 L23: 0.5780 REMARK 3 S TENSOR REMARK 3 S11: -0.2741 S12: -0.0245 S13: -0.1907 REMARK 3 S21: -0.0536 S22: 0.1826 S23: -0.0826 REMARK 3 S31: -0.1235 S32: -0.2574 S33: 0.0732 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 3M8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058250. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-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 : 42216 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.108 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.970 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 10.04 REMARK 200 R MERGE FOR SHELL (I) : 0.87900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.590 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 (%): 44.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 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 30.17333 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 60.34667 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 60.34667 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 30.17333 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: 7640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 A 216 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 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 108 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 3.2 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 ARG A 328 145.85 -176.12 REMARK 500 ASP A 381 110.18 -167.97 REMARK 500 THR A 399 -158.82 -104.02 REMARK 500 VAL A 433 -74.12 -126.28 REMARK 500 HIS A 526 137.55 -177.76 REMARK 500 TYR A 545 -57.85 -125.05 REMARK 500 VAL A 586 -17.90 -166.10 REMARK 500 GLN A 613 47.21 37.47 REMARK 500 HIS A 784 -67.29 70.67 REMARK 500 TYR A 811 90.42 -165.49 REMARK 500 LEU A 813 -169.17 -117.67 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 833 REMARK 610 15P A 6 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 27 O REMARK 620 2 HXZ A 113 O10 81.8 REMARK 620 3 HOH A 231 O 83.2 160.0 REMARK 620 4 ASP A 610 OD2 84.3 97.8 93.7 REMARK 620 5 ASP A 785 OD1 161.7 91.4 98.9 113.6 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 HXZ A 113 O7 REMARK 620 2 HXZ A 113 O10 97.6 REMARK 620 3 HXZ A 113 O9 82.2 84.8 REMARK 620 4 ASP A 610 OD1 98.6 106.5 168.3 REMARK 620 5 TYR A 611 O 87.4 172.2 89.9 78.5 REMARK 620 6 ASP A 785 OD2 166.5 92.9 90.3 86.4 81.3 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 HXZ 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 15P A 833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 15P A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3M8S RELATED DB: PDB REMARK 900 RELATED ID: 3KTQ RELATED DB: PDB REMARK 900 RELATED ID: 1QTM RELATED DB: PDB DBREF 3M8R A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 3M8R B 101 112 PDB 3M8R 3M8R 101 112 DBREF 3M8R C 201 216 PDB 3M8R 3M8R 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 3M8R DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC B 112 18 HET HXZ A 113 31 HET MG A 1 1 HET MG A 2 1 HET 15P A 833 13 HET GOL A 834 6 HET GOL A 5 6 HET 15P A 6 7 HET ACT A 7 4 HET GOL B 4 6 HET GOL C 3 6 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM HXZ 4'-ETHYLTHYMIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE) HETNAM MG MAGNESIUM ION HETNAM 15P POLYETHYLENE GLYCOL (N=34) HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETSYN 15P PEG 1500 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 HXZ C12 H21 N2 O14 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 15P 2(C69 H140 O35) FORMUL 8 GOL 4(C3 H8 O3) FORMUL 11 ACT C2 H3 O2 1- FORMUL 14 HOH *291(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 LEU A 522 1 8 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 GLY A 635 1 11 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 LEU A 682 1 9 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 SHEET 1 A 4 GLU A 295 ALA A 297 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 ARG A 328 -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 27 1555 1555 2.68 LINK MG MG A 1 O10 HXZ A 113 1555 1555 2.35 LINK MG MG A 1 O HOH A 231 1555 1555 2.36 LINK MG MG A 1 OD2 ASP A 610 1555 1555 2.31 LINK MG MG A 1 OD1 ASP A 785 1555 1555 2.15 LINK MG MG A 2 O7 HXZ A 113 1555 1555 1.84 LINK MG MG A 2 O10 HXZ A 113 1555 1555 1.95 LINK MG MG A 2 O9 HXZ A 113 1555 1555 2.07 LINK MG MG A 2 OD1 ASP A 610 1555 1555 2.01 LINK MG MG A 2 O TYR A 611 1555 1555 2.20 LINK MG MG A 2 OD2 ASP A 785 1555 1555 2.21 CISPEP 1 TRP A 299 PRO A 300 0 3.20 CISPEP 2 ASP A 578 PRO A 579 0 0.55 SITE 1 AC1 20 MG A 1 MG A 2 HOH A 27 HOH A 84 SITE 2 AC1 20 HOH A 160 ARG A 573 ASP A 610 TYR A 611 SITE 3 AC1 20 SER A 612 GLN A 613 ILE A 614 GLU A 615 SITE 4 AC1 20 HIS A 639 ARG A 659 LYS A 663 PHE A 667 SITE 5 AC1 20 ASP A 785 DOC B 112 DA C 204 DG C 205 SITE 1 AC2 7 MG A 2 HOH A 27 HXZ A 113 HOH A 231 SITE 2 AC2 7 ASP A 610 ASP A 785 DOC B 112 SITE 1 AC3 5 MG A 1 HXZ A 113 ASP A 610 TYR A 611 SITE 2 AC3 5 ASP A 785 SITE 1 AC4 14 ACT A 7 HOH A 49 HOH A 55 HOH A 226 SITE 2 AC4 14 GLU A 315 TRP A 318 LEU A 552 LEU A 560 SITE 3 AC4 14 HIS A 561 ASP A 578 PRO A 579 GOL A 834 SITE 4 AC4 14 DC C 209 DC C 210 SITE 1 AC5 10 HOH A 157 THR A 544 PRO A 548 LEU A 549 SITE 2 AC5 10 PRO A 579 ASN A 580 ASN A 583 15P A 833 SITE 3 AC5 10 DC C 209 DC C 210 SITE 1 AC6 11 HOH A 32 ASN A 485 SER A 486 ARG A 487 SITE 2 AC6 11 ASP A 488 HOH B 43 HOH B 165 DG C 211 SITE 3 AC6 11 DT C 212 DG C 213 HOH C 219 SITE 1 AC7 5 HOH A 50 HOH A 111 ARG A 450 GLU A 462 SITE 2 AC7 5 GLU A 602 SITE 1 AC8 4 ARG A 313 TRP A 318 LEU A 552 15P A 833 SITE 1 AC9 9 DC B 106 DG B 107 DG B 108 HOH B 114 SITE 2 AC9 9 HOH B 117 HOH B 246 HOH B 299 HOH C 103 SITE 3 AC9 9 DC C 209 SITE 1 BC1 4 HOH C 94 HOH C 185 DG C 205 DG C 206 CRYST1 108.789 108.789 90.520 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 0.009192 0.005307 0.000000 0.00000 SCALE2 0.000000 0.010614 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011047 0.00000