10 20 30 40 50 60 70 80 4BWM - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE/DNA/RNA 03-JUL-13 4BWM
TITLE KLENTAQ MUTANT IN COMPLEX WITH A RNA/DNA HYBRID
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; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOCP)-3'; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: PRIMER; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-R(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*UP*GP*GP*UP*C)-3'; COMPND 15 CHAIN: G; COMPND 16 SYNONYM: 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-RNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR N.BLATTER,K.BERGEN,W.WELTE,K.DIEDERICHS,A.MARX
REVDAT 3 23-SEP-15 4BWM 1 SOURCE JRNL REMARK REVDAT 2 25-DEC-13 4BWM 1 JRNL REVDAT 1 18-SEP-13 4BWM 0
JRNL AUTH N.BLATTER,K.BERGEN,O.NOLTE,W.WELTE,K.DIEDERICHS,J.MAYER, JRNL AUTH 2 M.WIELAND,A.MARX JRNL TITL STRUCTURE AND FUNCTION OF AN RNA-READING THERMOSTABLE DNA JRNL TITL 2 POLYMERASE. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 52 11935 2013 JRNL REFN ISSN 1433-7851 JRNL PMID 24106012 JRNL DOI 10.1002/ANIE.201306655
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.BLATTER,K.BERGEN,O.NOLTE,W.WELTE,K.DIEDERICHS, REMARK 1 AUTH 2 J.MAYER,M.WIELAND,A.MARX REMARK 1 TITL STRUKTUR UND FUNKTION EINER RNA-LESENDEN THERMOSTABILEN REMARK 1 TITL 2 DNA-POLYMERASE REMARK 1 REF ANGEW.CHEM. V. 125 12154 2013 REMARK 1 REFN ISSN 1433-7851 REMARK 1 DOI 10.1002/ANGE.201306655
REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1411) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.749 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.985 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.00 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.89 REMARK 3 NUMBER OF REFLECTIONS : 79632 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1700 REMARK 3 R VALUE (WORKING SET) : 0.1680 REMARK 3 FREE R VALUE : 0.2076 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 3989 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 48.0030 - 5.3081 1.00 2931 152 0.1625 0.2148 REMARK 3 2 5.3081 - 4.2140 1.00 2791 146 0.1368 0.1616 REMARK 3 3 4.2140 - 3.6815 1.00 2758 153 0.1336 0.1700 REMARK 3 4 3.6815 - 3.3450 1.00 2710 167 0.1495 0.1922 REMARK 3 5 3.3450 - 3.1053 1.00 2764 136 0.1722 0.2255 REMARK 3 6 3.1053 - 2.9223 1.00 2724 140 0.1793 0.2338 REMARK 3 7 2.9223 - 2.7759 1.00 2724 116 0.1794 0.2458 REMARK 3 8 2.7759 - 2.6551 1.00 2704 162 0.1827 0.2191 REMARK 3 9 2.6551 - 2.5529 1.00 2675 152 0.1806 0.2253 REMARK 3 10 2.5529 - 2.4648 1.00 2717 132 0.1743 0.2214 REMARK 3 11 2.4648 - 2.3877 1.00 2683 149 0.1697 0.2382 REMARK 3 12 2.3877 - 2.3195 1.00 2691 147 0.1716 0.1990 REMARK 3 13 2.3195 - 2.2584 1.00 2697 131 0.1717 0.2331 REMARK 3 14 2.2584 - 2.2033 1.00 2702 139 0.1617 0.1902 REMARK 3 15 2.2033 - 2.1532 1.00 2687 145 0.1629 0.1953 REMARK 3 16 2.1532 - 2.1074 1.00 2676 137 0.1671 0.2065 REMARK 3 17 2.1074 - 2.0653 1.00 2687 135 0.1777 0.1928 REMARK 3 18 2.0653 - 2.0263 1.00 2684 144 0.1799 0.2120 REMARK 3 19 2.0263 - 1.9901 1.00 2658 162 0.1944 0.2317 REMARK 3 20 1.9901 - 1.9564 1.00 2673 134 0.1944 0.2190 REMARK 3 21 1.9564 - 1.9248 1.00 2674 142 0.1963 0.2465 REMARK 3 22 1.9248 - 1.8952 1.00 2693 144 0.2093 0.2472 REMARK 3 23 1.8952 - 1.8673 1.00 2659 141 0.2153 0.2217 REMARK 3 24 1.8673 - 1.8410 1.00 2645 147 0.2255 0.2323 REMARK 3 25 1.8410 - 1.8161 1.00 2682 137 0.2316 0.2517 REMARK 3 26 1.8161 - 1.7925 1.00 2673 149 0.2429 0.2715 REMARK 3 27 1.7925 - 1.7701 1.00 2701 124 0.2481 0.2563 REMARK 3 28 1.7701 - 1.7488 0.97 2580 126 0.2574 0.2844 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) : 0.18 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.98 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 5043 REMARK 3 ANGLE : 1.089 6942 REMARK 3 CHIRALITY : 0.070 767 REMARK 3 PLANARITY : 0.005 819 REMARK 3 DIHEDRAL : 14.698 1992 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 295 THROUGH 433 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.1569 19.1825 2.6349 REMARK 3 T TENSOR REMARK 3 T11: 0.0950 T22: 0.0929 REMARK 3 T33: 0.1910 T12: -0.0075 REMARK 3 T13: -0.0233 T23: -0.0045 REMARK 3 L TENSOR REMARK 3 L11: 0.6949 L22: 0.1703 REMARK 3 L33: 0.2182 L12: -0.1149 REMARK 3 L13: 0.2941 L23: 0.0834 REMARK 3 S TENSOR REMARK 3 S11: -0.1084 S12: -0.0391 S13: 0.2061 REMARK 3 S21: 0.0246 S22: 0.0293 S23: -0.0949 REMARK 3 S31: -0.0345 S32: 0.0033 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 434 THROUGH 603 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.4906 -10.5362 -11.5175 REMARK 3 T TENSOR REMARK 3 T11: 0.1672 T22: 0.1011 REMARK 3 T33: 0.0803 T12: -0.0037 REMARK 3 T13: -0.0154 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.0607 L22: 0.0559 REMARK 3 L33: 0.3227 L12: -0.0310 REMARK 3 L13: 0.1173 L23: 0.0857 REMARK 3 S TENSOR REMARK 3 S11: 0.0375 S12: -0.0265 S13: 0.0176 REMARK 3 S21: -0.0829 S22: -0.0246 S23: -0.0472 REMARK 3 S31: 0.0744 S32: -0.0133 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 604 THROUGH 775 ) REMARK 3 ORIGIN FOR THE GROUP (A): -40.2541 7.9901 -11.8373 REMARK 3 T TENSOR REMARK 3 T11: 0.1234 T22: 0.1315 REMARK 3 T33: 0.1068 T12: 0.0099 REMARK 3 T13: -0.0446 T23: 0.0503 REMARK 3 L TENSOR REMARK 3 L11: 0.1809 L22: 0.4115 REMARK 3 L33: 0.7827 L12: -0.0230 REMARK 3 L13: 0.2235 L23: -0.4834 REMARK 3 S TENSOR REMARK 3 S11: 0.0355 S12: -0.0491 S13: 0.0509 REMARK 3 S21: -0.0987 S22: 0.1162 S23: 0.1101 REMARK 3 S31: 0.0867 S32: -0.0837 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESID 776 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.0566 -0.1513 8.8692 REMARK 3 T TENSOR REMARK 3 T11: 0.0889 T22: 0.1381 REMARK 3 T33: 0.1055 T12: 0.0139 REMARK 3 T13: 0.0069 T23: 0.0261 REMARK 3 L TENSOR REMARK 3 L11: 0.1520 L22: 0.0803 REMARK 3 L33: 0.1337 L12: -0.0355 REMARK 3 L13: 0.0486 L23: 0.0411 REMARK 3 S TENSOR REMARK 3 S11: 0.0146 S12: -0.0535 S13: -0.0461 REMARK 3 S21: 0.0474 S22: 0.0283 S23: 0.0881 REMARK 3 S31: 0.0226 S32: -0.0845 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND (RESID 103 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.7143 0.9984 -22.9811 REMARK 3 T TENSOR REMARK 3 T11: 0.2580 T22: 0.1896 REMARK 3 T33: 0.1345 T12: -0.0434 REMARK 3 T13: -0.0018 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: -0.0060 L22: 0.0165 REMARK 3 L33: 0.0698 L12: 0.0170 REMARK 3 L13: 0.0266 L23: 0.0063 REMARK 3 S TENSOR REMARK 3 S11: 0.0520 S12: 0.0399 S13: 0.4698 REMARK 3 S21: 0.0659 S22: 0.1924 S23: 0.0056 REMARK 3 S31: 0.4443 S32: -0.0375 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN G AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.6765 2.4380 -23.8398 REMARK 3 T TENSOR REMARK 3 T11: 0.1179 T22: 0.3239 REMARK 3 T33: 0.1450 T12: -0.0159 REMARK 3 T13: 0.0032 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: -0.0659 L22: -0.0816 REMARK 3 L33: 0.0791 L12: -0.0533 REMARK 3 L13: 0.0036 L23: 0.0407 REMARK 3 S TENSOR REMARK 3 S11: -0.2869 S12: 0.2763 S13: 0.2177 REMARK 3 S21: 0.1365 S22: 0.1423 S23: -0.0839 REMARK 3 S31: -0.0042 S32: 0.1191 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES 15 AND 16 OF THE REMARK 3 TEMPLATE AND 1 AND 2 OF THE PRIMER ARE DISORDERED
REMARK 4 REMARK 4 4BWM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUL-13. REMARK 100 THE PDBE ID CODE IS EBI-57573.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 1.000040 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 (PILATUS 6M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79729 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.75 REMARK 200 RESOLUTION RANGE LOW (A) : 47.34 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.59 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.73 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.62 REMARK 200 R MERGE FOR SHELL (I) : 1.12 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.70 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 3RTV REMARK 200 REMARK 200 REMARK: NONE
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.7 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP. 100MM TRIS PH8.5, REMARK 280 200MM MG-FORMATE, 20% PEG 8K MICROSEEDED
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 71.59600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.14100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 71.59600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.14100 REMARK 290 SMTRY3 4 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: 6740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, G 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 465 LEU A 294 REMARK 465 DG B 101 REMARK 465 DA B 102 REMARK 465 U G 15 REMARK 465 C G 16
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH1B ARG A 515 O HOH A 2305 2.15 REMARK 500 OD1 ASP A 551 O HOH A 2223 2.13 REMARK 500 OD1 ASP A 578 O HOH A 2394 2.14 REMARK 500 O HOH A 2153 O HOH A 2165 2.20 REMARK 500 O HOH A 2164 O HOH A 2180 2.15 REMARK 500 O HOH A 2181 O HOH A 2182 2.18 REMARK 500 O HOH A 2413 O HOH A 2419 2.15 REMARK 500 O HOH A 2429 O HOH A 2432 1.97 REMARK 500 O HOH G 2010 O HOH G 2018 2.18 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 DG B 110 C3' - C2' - C1' ANGL. DEV. = -5.0 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 381 116.13 -166.73 REMARK 500 VAL A 433 -66.72 -122.59 REMARK 500 ASP A 496 -62.75 -92.70 REMARK 500 TYR A 545 -56.20 -123.04 REMARK 500 HIS A 784 -123.44 53.59 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 A1836 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DCT A1833 O1G REMARK 620 2 HOH A2425 O 83.5 REMARK 620 3 DCT A1833 O1B 94.2 90.9 REMARK 620 4 DCT A1833 O2A 95.3 178.8 89.0 REMARK 620 5 HOH A2423 O 87.5 87.2 177.3 93.0 REMARK 620 6 HOH A2426 O 167.9 84.8 82.8 96.4 95.0 REMARK 620 N 1 2 3 4 5 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 B2025 O REMARK 620 2 DC B 111 OP1 98.3 REMARK 620 N 1 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 B2002 O REMARK 620 2 HOH B2006 O 92.0 REMARK 620 3 HOH B2027 O 168.0 81.3 REMARK 620 4 HOH B2028 O 89.1 82.3 80.1 REMARK 620 5 HOH B2029 O 92.8 166.7 91.6 85.4 REMARK 620 6 HOH B2001 O 87.5 97.4 103.2 176.6 95.2 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 DCT A1833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1836 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A1837 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A1838 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A1839 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1112 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1113 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT G1015
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BWJ RELATED DB: PDB REMARK 900 KLENTAQ MUTANT IN COMPLEX WITH DNA AND DDCTP
REMARK 999 REMARK 999 SEQUENCE REMARK 999 N-TERMINALLY TRUNCATED, KLENOW FRAGMENT
DBREF 4BWM A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4BWM B 101 112 PDB 4BWM 4BWM 101 112 DBREF 4BWM G 1 16 PDB 4BWM 4BWM 1 16
SEQADV 4BWM MET A 459 UNP P19821 LEU 459 ENGINEERED MUTATION SEQADV 4BWM ARG A 515 UNP P19821 SER 515 ENGINEERED MUTATION SEQADV 4BWM PHE A 638 UNP P19821 ILE 638 ENGINEERED MUTATION SEQADV 4BWM LYS A 747 UNP P19821 MET 747 ENGINEERED MUTATION
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 MET 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 ARG 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 PHE 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 LYS 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 G 16 A A A G G G C G C C G U G SEQRES 2 G 16 G U C
MODRES 4BWM DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
HET DOC B 112 18 HET DCT A1833 27 HET CL A1834 1 HET CL A1835 1 HET MG A1836 1 HET FMT A1837 3 HET FMT A1838 3 HET FMT A1839 3 HET MG B1112 1 HET MG B1113 1 HET FMT G1015 3
HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM CL CHLORIDE ION HETNAM DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE HETNAM FMT FORMIC ACID HETNAM MG MAGNESIUM ION
FORMUL 4 DOC C9 H14 N3 O6 P FORMUL 5 CL 2(CL 1-) FORMUL 6 DCT C9 H16 N3 O12 P3 FORMUL 7 FMT 4(C H2 O2) FORMUL 8 MG 3(MG 2+) FORMUL 9 HOH *631(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 ARG A 515 LEU A 522 1 8 HELIX 12 12 PRO A 527 TYR A 545 1 19 HELIX 13 13 ASP A 547 LEU A 552 1 6 HELIX 14 14 ASN A 580 ILE A 584 5 5 HELIX 15 15 THR A 588 ALA A 597 1 10 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 TYR A 671 1 17 HELIX 21 21 SER A 674 LEU A 682 1 9 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 GLU A 832 1 7
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 ILE A 553 HIS A 554 0 SHEET 2 AC 2 ARG A 559 LEU A 560 -1 O ARG A 559 N HIS A 554 SHEET 1 AD 2 ARG A 563 ASN A 565 0 SHEET 2 AD 2 SER A 575 SER A 577 -1 O SER A 575 N ASN A 565 SHEET 1 AE 4 ARG A 778 VAL A 783 0 SHEET 2 AE 4 GLU A 786 PRO A 792 -1 O GLU A 786 N VAL A 783 SHEET 3 AE 4 TRP A 604 TYR A 611 -1 O LEU A 605 N ALA A 791 SHEET 4 AE 4 VAL A 819 GLY A 824 -1 O GLU A 820 N ASP A 610 SHEET 1 AF 2 TYR A 719 GLU A 721 0 SHEET 2 AF 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720
LINK O2A DCT A1833 MG MG A1836 1555 1555 1.98 LINK O1B DCT A1833 MG MG A1836 1555 1555 2.09 LINK O1G DCT A1833 MG MG A1836 1555 1555 1.92 LINK MG MG A1836 O HOH A2425 1555 1555 2.07 LINK MG MG A1836 O HOH A2423 1555 1555 2.11 LINK MG MG A1836 O HOH A2426 1555 1555 1.94 LINK P DOC B 112 O3' DC B 111 1555 1555 1.58 LINK MG MG B1112 OP1 DC B 111 1555 1555 2.22 LINK MG MG B1112 O HOH B2025 1555 1555 2.93 LINK MG MG B1113 O HOH B2006 1555 1555 2.17 LINK MG MG B1113 O HOH B2027 1555 1555 2.16 LINK MG MG B1113 O HOH B2028 1555 1555 2.40 LINK MG MG B1113 O HOH B2029 1555 1555 2.16 LINK MG MG B1113 O HOH B2001 1555 1555 2.10 LINK MG MG B1113 O HOH B2002 1555 1555 2.26
CISPEP 1 TRP A 299 PRO A 300 0 1.10 CISPEP 2 ASP A 578 PRO A 579 0 5.10
SITE 1 AC1 20 GLN A 613 HIS A 639 ARG A 659 LYS A 663 SITE 2 AC1 20 PHE A 667 ASP A 785 MG A1836 HOH A2381 SITE 3 AC1 20 HOH A2423 HOH A2425 HOH A2426 HOH A2429 SITE 4 AC1 20 HOH A2430 HOH A2433 HOH A2546 HOH A2581 SITE 5 AC1 20 HOH A2582 DOC B 112 G G 4 G G 5 SITE 1 AC2 1 ARG A 559 SITE 1 AC3 3 VAL A 730 PRO A 731 ASP A 732 SITE 1 AC4 4 DCT A1833 HOH A2423 HOH A2425 HOH A2426 SITE 1 AC5 5 GLU A 424 LEU A 427 ARG A 431 HOH A2452 SITE 2 AC5 5 HOH A2453 SITE 1 AC6 3 ASP A 371 ARG A 435 HOH A2161 SITE 1 AC7 4 TYR A 545 ASN A 583 HOH A2396 HOH A2398 SITE 1 AC8 3 DG B 110 DC B 111 HOH B2025 SITE 1 AC9 6 HOH B2001 HOH B2002 HOH B2006 HOH B2027 SITE 2 AC9 6 HOH B2028 HOH B2029 SITE 1 BC1 5 GLN A 582 HOH A2380 HOH A2386 G G 6 SITE 2 BC1 5 C G 7
CRYST1 143.192 86.282 63.094 90.00 90.00 90.00 P 21 21 2 4
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 0.006984 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011590 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015849 0.00000