HEADER DNA BINDING PROTEIN 19-DEC-17 6FBF TITLE KLENTAQ DNA POLYMERASE PROCESSING A MODIFIED PRIMER - BEARING THE TITLE 2 MODIFICATION UPSTREAM AT THE FOURTH PRIMER NUCLEOTIDE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TAQ POLYMERASE 1; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*GP*CP*AP*(OH3)P*CP*GP*C)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*AP*AP*AP*CP*GP*CP*GP*GP*TP*GP*CP*TP*GP*GP*TP*C)- COMPND 13 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 GENE: POLA, POL1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, MODIFIED NUCLEOTIDES, KLENTAQ, KLENTAQ DNA KEYWDS 2 POLYMERASE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.M.KROPP,K.DIEDERICHS,A.MARX REVDAT 3 14-AUG-19 6FBF 1 COMPND REMARK REVDAT 2 10-OCT-18 6FBF 1 COMPND JRNL REVDAT 1 26-SEP-18 6FBF 0 JRNL AUTH H.M.KROPP,S.L.DURR,C.PETER,K.DIEDERICHS,A.MARX JRNL TITL SNAPSHOTS OF A MODIFIED NUCLEOTIDE MOVING THROUGH THE JRNL TITL 2 CONFINES OF A DNA POLYMERASE. JRNL REF PROC. NATL. ACAD. SCI. V. 115 9992 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 30224478 JRNL DOI 10.1073/PNAS.1811518115 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12RC1_2815: ???) 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) : 47.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.140 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 81885 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 4128 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 47.3458 - 6.1434 1.00 2672 156 0.1756 0.1757 REMARK 3 2 6.1434 - 4.8778 1.00 2700 146 0.1638 0.2019 REMARK 3 3 4.8778 - 4.2617 1.00 2714 125 0.1370 0.1813 REMARK 3 4 4.2617 - 3.8722 1.00 2641 171 0.1497 0.1628 REMARK 3 5 3.8722 - 3.5948 1.00 2699 178 0.1641 0.2200 REMARK 3 6 3.5948 - 3.3829 1.00 2648 151 0.1746 0.1750 REMARK 3 7 3.3829 - 3.2135 1.00 2695 130 0.2010 0.2245 REMARK 3 8 3.2135 - 3.0737 1.00 2703 152 0.2185 0.2336 REMARK 3 9 3.0737 - 2.9554 1.00 2654 137 0.2304 0.2191 REMARK 3 10 2.9554 - 2.8534 1.00 2716 146 0.2237 0.2420 REMARK 3 11 2.8534 - 2.7642 1.00 2701 152 0.2314 0.3080 REMARK 3 12 2.7642 - 2.6852 1.00 2655 147 0.2384 0.2506 REMARK 3 13 2.6852 - 2.6145 1.00 2703 160 0.2495 0.2847 REMARK 3 14 2.6145 - 2.5507 1.00 2672 130 0.2418 0.2791 REMARK 3 15 2.5507 - 2.4927 1.00 2678 167 0.2285 0.3144 REMARK 3 16 2.4927 - 2.4397 1.00 2704 135 0.2256 0.2685 REMARK 3 17 2.4397 - 2.3909 1.00 2661 127 0.2368 0.2830 REMARK 3 18 2.3909 - 2.3458 1.00 2755 120 0.2384 0.2738 REMARK 3 19 2.3458 - 2.3039 1.00 2709 129 0.2503 0.2455 REMARK 3 20 2.3039 - 2.2648 1.00 2672 154 0.2321 0.2791 REMARK 3 21 2.2648 - 2.2283 1.00 2684 125 0.2431 0.2979 REMARK 3 22 2.2283 - 2.1940 1.00 2730 123 0.2550 0.2614 REMARK 3 23 2.1940 - 2.1617 1.00 2674 142 0.2488 0.2541 REMARK 3 24 2.1617 - 2.1313 1.00 2739 118 0.2564 0.3180 REMARK 3 25 2.1313 - 2.1025 1.00 2673 139 0.2785 0.3351 REMARK 3 26 2.1025 - 2.0752 1.00 2737 131 0.2756 0.3256 REMARK 3 27 2.0752 - 2.0493 1.00 2678 135 0.2693 0.2573 REMARK 3 28 2.0493 - 2.0246 1.00 2632 159 0.2947 0.2747 REMARK 3 29 2.0246 - 2.0010 0.91 2458 143 0.3073 0.3684 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.004 4925 REMARK 3 ANGLE : 0.523 6799 REMARK 3 CHIRALITY : 0.038 764 REMARK 3 PLANARITY : 0.003 819 REMARK 3 DIHEDRAL : 13.853 2871 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 THROUGH 433 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.0746 -42.8963 -17.5920 REMARK 3 T TENSOR REMARK 3 T11: 0.2687 T22: 0.2583 REMARK 3 T33: 0.4895 T12: -0.0572 REMARK 3 T13: 0.0492 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 2.7027 L22: 1.7645 REMARK 3 L33: 1.3938 L12: -0.1375 REMARK 3 L13: 0.1736 L23: -0.0568 REMARK 3 S TENSOR REMARK 3 S11: 0.0373 S12: -0.1733 S13: -0.7273 REMARK 3 S21: -0.2032 S22: 0.0039 S23: -0.2509 REMARK 3 S31: 0.1469 S32: 0.0432 S33: -0.0428 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 434 THROUGH 562 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.0249 -11.2948 2.5871 REMARK 3 T TENSOR REMARK 3 T11: 0.5338 T22: 0.2231 REMARK 3 T33: 0.2973 T12: 0.0219 REMARK 3 T13: 0.0745 T23: 0.0155 REMARK 3 L TENSOR REMARK 3 L11: 1.2823 L22: 1.3283 REMARK 3 L33: 2.3765 L12: 0.9677 REMARK 3 L13: -0.6250 L23: -0.3761 REMARK 3 S TENSOR REMARK 3 S11: 0.2938 S12: -0.1857 S13: 0.1934 REMARK 3 S21: 0.1499 S22: -0.1437 S23: 0.0630 REMARK 3 S31: -1.0683 S32: 0.0594 S33: -0.1213 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 563 THROUGH 831 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.3434 -20.5616 -11.7156 REMARK 3 T TENSOR REMARK 3 T11: 0.3517 T22: 0.5285 REMARK 3 T33: 0.2492 T12: 0.1904 REMARK 3 T13: 0.0289 T23: 0.0587 REMARK 3 L TENSOR REMARK 3 L11: 1.6984 L22: 1.5708 REMARK 3 L33: 2.7302 L12: 0.0564 REMARK 3 L13: 0.7232 L23: -0.4015 REMARK 3 S TENSOR REMARK 3 S11: -0.1683 S12: -0.1996 S13: 0.0048 REMARK 3 S21: -0.1053 S22: 0.2810 S23: 0.2155 REMARK 3 S31: -0.6520 S32: -0.9663 S33: -0.0830 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 108 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.5959 -26.6588 7.7104 REMARK 3 T TENSOR REMARK 3 T11: 0.3136 T22: 0.4048 REMARK 3 T33: 0.4626 T12: 0.0949 REMARK 3 T13: -0.0052 T23: 0.0609 REMARK 3 L TENSOR REMARK 3 L11: 5.2346 L22: 3.4046 REMARK 3 L33: 0.4951 L12: -0.2823 REMARK 3 L13: -0.7928 L23: 0.6846 REMARK 3 S TENSOR REMARK 3 S11: -0.1209 S12: 0.9465 S13: -0.8692 REMARK 3 S21: 0.4881 S22: -0.3695 S23: -0.2292 REMARK 3 S31: 0.3725 S32: 0.1998 S33: 0.4241 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 110 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.2020 -15.8573 -4.9784 REMARK 3 T TENSOR REMARK 3 T11: 0.4140 T22: 0.4074 REMARK 3 T33: 0.3238 T12: 0.1429 REMARK 3 T13: 0.0095 T23: 0.0171 REMARK 3 L TENSOR REMARK 3 L11: 1.9234 L22: 3.2843 REMARK 3 L33: 1.1517 L12: 1.8516 REMARK 3 L13: 0.6912 L23: 1.4941 REMARK 3 S TENSOR REMARK 3 S11: -0.0944 S12: -0.0015 S13: 0.2328 REMARK 3 S21: 0.1877 S22: 0.2595 S23: 0.1975 REMARK 3 S31: -0.2631 S32: -0.2756 S33: -0.1317 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 201 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6431 -21.2589 7.2726 REMARK 3 T TENSOR REMARK 3 T11: 0.4921 T22: 0.8410 REMARK 3 T33: 0.3692 T12: 0.2103 REMARK 3 T13: 0.0440 T23: 0.0722 REMARK 3 L TENSOR REMARK 3 L11: 0.9873 L22: 9.7845 REMARK 3 L33: 3.9544 L12: -1.1307 REMARK 3 L13: 1.1667 L23: 3.3376 REMARK 3 S TENSOR REMARK 3 S11: -0.2743 S12: -0.2503 S13: 0.4848 REMARK 3 S21: 1.3661 S22: -0.1433 S23: 0.0208 REMARK 3 S31: 0.1274 S32: -0.4522 S33: 0.3360 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 206 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.5552 -23.9481 5.9942 REMARK 3 T TENSOR REMARK 3 T11: 0.2859 T22: 0.2747 REMARK 3 T33: 0.3071 T12: 0.0761 REMARK 3 T13: -0.0119 T23: 0.0502 REMARK 3 L TENSOR REMARK 3 L11: 1.3605 L22: 2.4047 REMARK 3 L33: 0.9952 L12: -0.7969 REMARK 3 L13: -1.0434 L23: 0.1572 REMARK 3 S TENSOR REMARK 3 S11: -0.3046 S12: -0.4110 S13: -0.1634 REMARK 3 S21: 0.3403 S22: 0.3326 S23: -0.4014 REMARK 3 S31: -0.2376 S32: -0.0720 S33: -0.0677 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 6FBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007859. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81905 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.001 REMARK 200 RESOLUTION RANGE LOW (A) : 47.333 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.360 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5300 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) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.34 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.870 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16 % PEG 4000, 20 MM MANGANESE(II) REMARK 280 CHLORIDE, 0.1 M TRIS, 0.1 M SODIUM ACETATE, PH 6.0, VAPOR REMARK 280 DIFFUSION, 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 30.37433 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 60.74867 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 60.74867 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 30.37433 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: 5900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 MET A 292 REMARK 465 ALA A 293 REMARK 465 GLU A 832 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 303 CG CD OE1 OE2 REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 ARG A 392 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 397 CG CD OE1 OE2 REMARK 470 ARG A 411 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 421 CG CD OE1 OE2 REMARK 470 GLU A 424 CG CD OE1 OE2 REMARK 470 ARG A 469 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 498 CG CD1 CD2 REMARK 470 GLU A 520 CG CD OE1 OE2 REMARK 470 ARG A 523 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 524 CG CD OE1 OE2 REMARK 470 GLU A 530 CG CD OE1 OE2 REMARK 470 LYS A 531 CG CD CE NZ REMARK 470 ARG A 556 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 587 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 630 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 676 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 680 CG CD OE1 NE2 REMARK 470 GLU A 687 CG CD OE1 OE2 REMARK 470 GLN A 690 CG CD OE1 NE2 REMARK 470 GLU A 694 CG CD OE1 OE2 REMARK 470 ARG A 695 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 698 CG CD OE1 NE2 REMARK 470 LYS A 702 CG CD CE NZ REMARK 470 LYS A 709 CG CD CE NZ REMARK 470 GLU A 713 CG CD OE1 OE2 REMARK 470 ARG A 736 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 774 CG CD OE1 OE2 REMARK 470 ARG A 795 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 797 CG CD OE1 OE2 REMARK 470 ARG A 801 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 831 CG CD CE NZ 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 HH12 ARG A 659 O3G XG4 A 903 1.60 REMARK 500 OD1 ASP A 320 HH TYR A 339 1.60 REMARK 500 O HOH A 1157 O HOH A 1196 2.10 REMARK 500 O HIS A 526 O HOH A 1001 2.10 REMARK 500 O HOH B 212 O HOH C 314 2.19 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 DA B 108 C3' - O3' - P ANGL. DEV. = -8.8 DEGREES REMARK 500 D4B B 109 O3' - P - OP1 ANGL. DEV. = 16.5 DEGREES REMARK 500 DC B 110 O3' - P - OP2 ANGL. DEV. = 18.1 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 381 111.11 -163.37 REMARK 500 THR A 399 -162.77 -106.22 REMARK 500 VAL A 433 -73.37 -126.44 REMARK 500 TYR A 545 -59.45 -128.01 REMARK 500 VAL A 586 -25.19 -168.38 REMARK 500 HIS A 784 -60.72 74.37 REMARK 500 TYR A 811 91.85 -161.41 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 MN A 902 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 75.1 REMARK 620 3 ASP A 785 OD2 91.0 95.0 REMARK 620 4 XG4 A 903 O1A 98.4 170.9 78.6 REMARK 620 5 XG4 A 903 O1B 175.2 102.2 93.2 84.8 REMARK 620 6 XG4 A 903 O1G 86.7 86.2 177.0 99.8 89.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 901 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 ASP A 785 OD1 100.6 REMARK 620 3 DC B 112 O3' 166.5 74.1 REMARK 620 4 XG4 A 903 O1A 105.7 89.8 86.9 REMARK 620 5 HOH A1026 O 88.1 94.0 80.1 164.8 REMARK 620 6 HOH A1045 O 90.3 169.1 95.4 86.9 86.6 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 MN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XG4 A 903 DBREF 6FBF A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 6FBF B 101 112 PDB 6FBF 6FBF 101 112 DBREF 6FBF C 201 216 PDB 6FBF 6FBF 201 216 SEQADV 6FBF MET A 292 UNP P19821 INITIATING METHIONINE SEQRES 1 A 541 MET ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY SEQRES 2 A 541 ALA PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET SEQRES 3 A 541 TRP ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY SEQRES 4 A 541 ARG VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG SEQRES 5 A 541 ASP LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SEQRES 6 A 541 SER VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO SEQRES 7 A 541 GLY ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SEQRES 8 A 541 SER ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY SEQRES 9 A 541 GLY GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SEQRES 10 A 541 SER GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU SEQRES 11 A 541 GLY GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU SEQRES 12 A 541 ARG PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR SEQRES 13 A 541 GLY VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER SEQRES 14 A 541 LEU GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU SEQRES 15 A 541 VAL PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER SEQRES 16 A 541 ARG ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY SEQRES 17 A 541 LEU PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SEQRES 18 A 541 SER THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA SEQRES 19 A 541 HIS PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU SEQRES 20 A 541 THR LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP SEQRES 21 A 541 LEU ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE SEQRES 22 A 541 ASN GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER SEQRES 23 A 541 ASP PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU SEQRES 24 A 541 GLY GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY SEQRES 25 A 541 TRP LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU SEQRES 26 A 541 ARG VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE SEQRES 27 A 541 ARG VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR SEQRES 28 A 541 ALA SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP SEQRES 29 A 541 PRO LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY SEQRES 30 A 541 VAL LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU SEQRES 31 A 541 LEU ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU SEQRES 32 A 541 ARG TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE SEQRES 33 A 541 GLU LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL SEQRES 34 A 541 GLU THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU SEQRES 35 A 541 GLU ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG SEQRES 36 A 541 MET ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP SEQRES 37 A 541 LEU MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU SEQRES 38 A 541 GLU GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP SEQRES 39 A 541 GLU LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA SEQRES 40 A 541 VAL ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR SEQRES 41 A 541 PRO LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY SEQRES 42 A 541 GLU ASP TRP LEU SER ALA LYS GLU SEQRES 1 B 12 DG DA DC DC DA DG DC DA D4B DC DG DC SEQRES 1 C 16 DA DA DA DC DG DC DG DG DT DG DC DT DG SEQRES 2 C 16 DG DT DC HET D4B B 109 44 HET MN A 901 1 HET MN A 902 1 HET XG4 A 903 44 HETNAM D4B [(2~{R},3~{S},5~{R})-5-[4-AZANYL-5-[2-(4- HETNAM 2 D4B ETHYNYLPHENYL)ETHYNYL]-2-OXIDANYLIDENE-PYRIMIDIN-1- HETNAM 3 D4B YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM XG4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 XG4 PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE FORMUL 2 D4B C19 H18 N3 O7 P FORMUL 4 MN 2(MN 2+) FORMUL 6 XG4 C10 H17 N6 O12 P3 FORMUL 7 HOH *265(H2 O) HELIX 1 AA1 GLU A 337 ARG A 343 1 7 HELIX 2 AA2 LEU A 352 GLU A 363 1 12 HELIX 3 AA3 ASP A 372 ASP A 381 1 10 HELIX 4 AA4 THR A 386 GLY A 395 1 10 HELIX 5 AA5 GLU A 401 LEU A 420 1 20 HELIX 6 AA6 GLU A 423 VAL A 433 1 11 HELIX 7 AA7 VAL A 433 GLY A 448 1 16 HELIX 8 AA8 ASP A 452 GLY A 479 1 28 HELIX 9 AA9 SER A 486 ASP A 496 1 11 HELIX 10 AB1 SER A 515 LEU A 522 1 8 HELIX 11 AB2 HIS A 526 TYR A 545 1 20 HELIX 12 AB3 PRO A 548 ILE A 553 5 6 HELIX 13 AB4 THR A 588 ARG A 596 1 9 HELIX 14 AB5 GLN A 613 GLY A 624 1 12 HELIX 15 AB6 ASP A 625 GLU A 634 1 10 HELIX 16 AB7 ASP A 637 GLY A 648 1 12 HELIX 17 AB8 PRO A 650 VAL A 654 5 5 HELIX 18 AB9 ASP A 655 TYR A 671 1 17 HELIX 19 AC1 SER A 674 ALA A 683 1 10 HELIX 20 AC2 PRO A 685 SER A 699 1 15 HELIX 21 AC3 PHE A 700 GLY A 718 1 19 HELIX 22 AC4 PRO A 731 ALA A 735 5 5 HELIX 23 AC5 VAL A 737 MET A 775 1 39 HELIX 24 AC6 ARG A 795 GLY A 809 1 15 HELIX 25 AC7 ASP A 826 LYS A 831 1 6 SHEET 1 AA1 4 GLU A 295 ALA A 297 0 SHEET 2 AA1 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 AA1 4 LEU A 321 ARG A 328 -1 N ALA A 326 O HIS A 333 SHEET 4 AA1 4 PHE A 306 LEU A 311 -1 N GLY A 308 O ALA A 325 SHEET 1 AA2 2 ARG A 450 LEU A 451 0 SHEET 2 AA2 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 AA3 2 ARG A 563 ASN A 565 0 SHEET 2 AA3 2 SER A 575 SER A 577 -1 O SER A 575 N ASN A 565 SHEET 1 AA4 4 ARG A 778 GLN A 782 0 SHEET 2 AA4 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 AA4 4 TRP A 604 TYR A 611 -1 N VAL A 607 O LEU A 789 SHEET 4 AA4 4 VAL A 819 GLY A 824 -1 O GLY A 824 N LEU A 606 SHEET 1 AA5 2 TYR A 719 GLU A 721 0 SHEET 2 AA5 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK OD1 ASP A 610 MN MN A 902 1555 1555 2.13 LINK OD2 ASP A 610 MN MN A 901 1555 1555 2.17 LINK O TYR A 611 MN MN A 902 1555 1555 2.07 LINK OD1 ASP A 785 MN MN A 901 1555 1555 2.15 LINK OD2 ASP A 785 MN MN A 902 1555 1555 2.14 LINK O3' DA B 108 P D4B B 109 1555 1555 1.60 LINK O3' D4B B 109 P DC B 110 1555 1555 1.60 LINK O3' DC B 112 MN MN A 901 1555 1555 2.32 LINK MN MN A 901 O1A XG4 A 903 1555 1555 2.22 LINK MN MN A 901 O HOH A1026 1555 1555 2.18 LINK MN MN A 901 O HOH A1045 1555 1555 2.20 LINK MN MN A 902 O1A XG4 A 903 1555 1555 2.23 LINK MN MN A 902 O1B XG4 A 903 1555 1555 2.06 LINK MN MN A 902 O1G XG4 A 903 1555 1555 2.12 CISPEP 1 TRP A 299 PRO A 300 0 1.11 CISPEP 2 ASP A 578 PRO A 579 0 -2.80 SITE 1 AC1 7 ASP A 610 ASP A 785 MN A 902 XG4 A 903 SITE 2 AC1 7 HOH A1026 HOH A1045 DC B 112 SITE 1 AC2 5 ASP A 610 TYR A 611 ASP A 785 MN A 901 SITE 2 AC2 5 XG4 A 903 SITE 1 AC3 23 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC3 23 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC3 23 ARG A 659 ARG A 660 LYS A 663 PHE A 667 SITE 4 AC3 23 TYR A 671 ASP A 785 MN A 901 MN A 902 SITE 5 AC3 23 HOH A1022 HOH A1045 HOH A1067 HOH A1148 SITE 6 AC3 23 DC B 112 DC C 204 DG C 205 CRYST1 109.310 109.310 91.123 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 0.009148 0.005282 0.000000 0.00000 SCALE2 0.000000 0.010564 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010974 0.00000