HEADER DNA BINDING PROTEIN 19-DEC-17 6FBI TITLE KLENTAQ DNA POLYMERASE IN A CLOSED, TERNARY COMPLEX WITH DGPNHPP BOUND TITLE 2 IN THE ACTIVE SITE 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*CP*GP*GP*CP*CP*AP*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*TP*GP*GP*CP*CP*GP*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 6FBI 1 COMPND REMARK REVDAT 2 10-OCT-18 6FBI 1 COMPND JRNL REVDAT 1 26-SEP-18 6FBI 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. 1.90 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 96941 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 4891 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 47.5467 - 5.8999 1.00 3068 182 0.1542 0.1575 REMARK 3 2 5.8999 - 4.6843 1.00 3075 158 0.1487 0.1768 REMARK 3 3 4.6843 - 4.0925 1.00 3074 158 0.1372 0.1810 REMARK 3 4 4.0925 - 3.7185 1.00 3058 197 0.1642 0.2146 REMARK 3 5 3.7185 - 3.4521 1.00 3046 184 0.1836 0.1943 REMARK 3 6 3.4521 - 3.2486 1.00 3062 169 0.1958 0.2232 REMARK 3 7 3.2486 - 3.0859 1.00 3097 162 0.2154 0.2192 REMARK 3 8 3.0859 - 2.9516 1.00 3091 156 0.2276 0.2719 REMARK 3 9 2.9516 - 2.8380 1.00 3068 169 0.2435 0.2775 REMARK 3 10 2.8380 - 2.7401 1.00 3051 165 0.2394 0.2515 REMARK 3 11 2.7401 - 2.6544 1.00 3106 174 0.2437 0.2859 REMARK 3 12 2.6544 - 2.5785 1.00 3028 179 0.2377 0.3247 REMARK 3 13 2.5785 - 2.5107 1.00 3033 177 0.2411 0.2914 REMARK 3 14 2.5107 - 2.4494 1.00 3122 155 0.2260 0.2535 REMARK 3 15 2.4494 - 2.3937 1.00 3097 146 0.2250 0.2626 REMARK 3 16 2.3937 - 2.3428 1.00 3026 134 0.2322 0.2649 REMARK 3 17 2.3428 - 2.2959 1.00 3156 155 0.2540 0.2839 REMARK 3 18 2.2959 - 2.2526 1.00 3091 169 0.2867 0.2955 REMARK 3 19 2.2526 - 2.2124 1.00 3122 134 0.3096 0.3383 REMARK 3 20 2.2124 - 2.1749 1.00 2997 159 0.2570 0.2864 REMARK 3 21 2.1749 - 2.1398 1.00 3137 138 0.2599 0.2831 REMARK 3 22 2.1398 - 2.1069 1.00 3058 155 0.2772 0.3469 REMARK 3 23 2.1069 - 2.0759 1.00 3089 151 0.2772 0.2748 REMARK 3 24 2.0759 - 2.0466 1.00 3076 157 0.3039 0.3047 REMARK 3 25 2.0466 - 2.0190 1.00 3070 186 0.2973 0.3661 REMARK 3 26 2.0190 - 1.9928 1.00 3063 183 0.3057 0.3189 REMARK 3 27 1.9928 - 1.9678 1.00 3082 171 0.3160 0.3186 REMARK 3 28 1.9678 - 1.9441 1.00 3082 160 0.3258 0.3422 REMARK 3 29 1.9441 - 1.9215 0.94 2873 154 0.4386 0.5451 REMARK 3 30 1.9215 - 1.8999 1.00 3052 154 0.5279 0.5356 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.430 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 4941 REMARK 3 ANGLE : 0.713 6829 REMARK 3 CHIRALITY : 0.043 765 REMARK 3 PLANARITY : 0.004 801 REMARK 3 DIHEDRAL : 15.951 2892 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 294 THROUGH 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.5384 -40.6135 -18.1776 REMARK 3 T TENSOR REMARK 3 T11: 0.3584 T22: 0.3536 REMARK 3 T33: 0.6310 T12: -0.1524 REMARK 3 T13: 0.1075 T23: -0.0480 REMARK 3 L TENSOR REMARK 3 L11: 1.7388 L22: 1.3185 REMARK 3 L33: 1.8757 L12: -0.1213 REMARK 3 L13: 0.1925 L23: 0.4292 REMARK 3 S TENSOR REMARK 3 S11: -0.0129 S12: 0.0500 S13: -0.7830 REMARK 3 S21: -0.2148 S22: 0.0829 S23: -0.3946 REMARK 3 S31: 0.3241 S32: -0.0840 S33: -0.0443 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 453 THROUGH 603 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.6848 -11.1594 1.6488 REMARK 3 T TENSOR REMARK 3 T11: 0.5283 T22: 0.2161 REMARK 3 T33: 0.3664 T12: 0.0585 REMARK 3 T13: 0.0369 T23: 0.0113 REMARK 3 L TENSOR REMARK 3 L11: 1.4600 L22: 1.4865 REMARK 3 L33: 2.5961 L12: 1.0268 REMARK 3 L13: -0.5701 L23: -0.3796 REMARK 3 S TENSOR REMARK 3 S11: 0.1683 S12: -0.1066 S13: 0.2159 REMARK 3 S21: 0.1074 S22: -0.0937 S23: 0.0050 REMARK 3 S31: -1.0940 S32: -0.2054 S33: -0.0356 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 604 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.6502 -21.3578 -11.8237 REMARK 3 T TENSOR REMARK 3 T11: 0.3466 T22: 0.9822 REMARK 3 T33: 0.3431 T12: 0.2088 REMARK 3 T13: -0.0164 T23: 0.0922 REMARK 3 L TENSOR REMARK 3 L11: 1.8579 L22: 1.3916 REMARK 3 L33: 2.9189 L12: 0.4945 REMARK 3 L13: 0.2451 L23: -0.2326 REMARK 3 S TENSOR REMARK 3 S11: -0.1051 S12: -0.1159 S13: 0.0522 REMARK 3 S21: -0.2314 S22: 0.2321 S23: 0.2451 REMARK 3 S31: -1.0198 S32: -1.6965 S33: -0.0652 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.0207 -23.1475 4.0723 REMARK 3 T TENSOR REMARK 3 T11: 0.2943 T22: 0.3485 REMARK 3 T33: 0.3535 T12: 0.0969 REMARK 3 T13: 0.0562 T23: 0.0716 REMARK 3 L TENSOR REMARK 3 L11: 3.7322 L22: 0.7216 REMARK 3 L33: 2.4538 L12: 1.4556 REMARK 3 L13: 0.5379 L23: -0.3460 REMARK 3 S TENSOR REMARK 3 S11: 0.1622 S12: 0.5475 S13: -0.4593 REMARK 3 S21: -0.1308 S22: -0.4501 S23: -0.2820 REMARK 3 S31: -0.2448 S32: 0.4686 S33: 0.1462 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 201 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.5740 -21.5470 7.1725 REMARK 3 T TENSOR REMARK 3 T11: 0.4672 T22: 1.3758 REMARK 3 T33: 0.4441 T12: 0.1974 REMARK 3 T13: -0.0279 T23: 0.0233 REMARK 3 L TENSOR REMARK 3 L11: 2.4636 L22: 6.5664 REMARK 3 L33: 0.6384 L12: 2.3343 REMARK 3 L13: -0.8461 L23: -2.0277 REMARK 3 S TENSOR REMARK 3 S11: -0.0184 S12: -1.9903 S13: 0.4590 REMARK 3 S21: 1.2553 S22: 0.1278 S23: -0.0340 REMARK 3 S31: -0.2555 S32: 0.0348 S33: 0.0893 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 206 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.5388 -24.0769 5.7726 REMARK 3 T TENSOR REMARK 3 T11: 0.2123 T22: 0.2511 REMARK 3 T33: 0.3225 T12: 0.0223 REMARK 3 T13: -0.0060 T23: 0.0849 REMARK 3 L TENSOR REMARK 3 L11: 1.4317 L22: 2.7519 REMARK 3 L33: 1.4270 L12: -0.6525 REMARK 3 L13: -1.4393 L23: 0.5455 REMARK 3 S TENSOR REMARK 3 S11: -0.0963 S12: -0.1741 S13: -0.2300 REMARK 3 S21: 0.2225 S22: 0.2701 S23: -0.3820 REMARK 3 S31: -0.0476 S32: -0.1957 S33: -0.1660 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 6FBI 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_1200007862. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5-7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA 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 PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 97132 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 47.532 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.95 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 14.58 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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 (%): 44.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (A) 16 % PEG 4000, 0.1 M SODIUM REMARK 280 ACETATE, 20 MM MANGANESE(II) CHLORIDE, 0.1 M MES (B) 17 % PEG REMARK 280 4000, 0.1 M AMMONIUM ACETATE, 0.1 M HEPES, 20 MM MANGANESE(II) REMARK 280 CHLORIDE (C) 15 % PEG 4000, 0.1 M SODIUM ACETATE, 20 MM REMARK 280 MANGANESE(II) CHLORIDE, 0.1 M MES, VAPOR DIFFUSION, TEMPERATURE REMARK 280 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 30.48667 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 60.97333 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 60.97333 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 30.48667 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: 6310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24180 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 A1150 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 MET A 292 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 295 CG CD OE1 OE2 REMARK 470 GLU A 303 CG CD OE1 OE2 REMARK 470 ARG A 331 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 ARG A 392 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 411 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 421 CG CD OE1 OE2 REMARK 470 GLU A 462 CG CD OE1 OE2 REMARK 470 GLU A 473 CG CD OE1 OE2 REMARK 470 GLU A 524 CG CD OE1 OE2 REMARK 470 GLU A 530 CG CD OE1 OE2 REMARK 470 ARG A 556 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 602 CG CD OE1 OE2 REMARK 470 ARG A 630 CG CD NE CZ NH1 NH2 REMARK 470 SER A 644 OG REMARK 470 VAL A 649 CG1 CG2 REMARK 470 GLU A 652 CG CD OE1 OE2 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 GLU A 694 CG CD OE1 OE2 REMARK 470 PHE A 697 CG CD1 CD2 CE1 CE2 CZ 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 797 CG CD OE1 OE2 REMARK 470 ARG A 801 CG CD NE CZ NH1 NH2 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 MN MN A 902 O HOH A 1001 1.57 REMARK 500 O PRO A 650 H ALA A 653 1.59 REMARK 500 O HOH A 1029 O HOH A 1052 2.01 REMARK 500 OP2 DT C 212 O HOH C 401 2.17 REMARK 500 OD2 ASP A 610 O HOH A 1001 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 DG B 108 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 2.6 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 328 146.19 -170.28 REMARK 500 ASP A 381 110.94 -165.63 REMARK 500 THR A 399 -158.87 -110.60 REMARK 500 VAL A 433 -67.92 -125.28 REMARK 500 ASP A 496 -62.10 -100.17 REMARK 500 HIS A 526 136.11 -174.74 REMARK 500 TYR A 545 -54.85 -124.61 REMARK 500 VAL A 586 -27.92 -150.77 REMARK 500 HIS A 784 -62.76 71.20 REMARK 500 TYR A 811 85.36 -168.15 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 903 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 73.0 REMARK 620 3 ASP A 785 OD2 89.0 95.5 REMARK 620 4 XG4 A 901 O1A 101.3 174.0 82.5 REMARK 620 5 XG4 A 901 O1B 168.0 98.2 100.1 87.7 REMARK 620 6 XG4 A 901 O3G 87.6 83.2 176.6 98.5 83.2 REMARK 620 N 1 2 3 4 5 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 OD2 REMARK 620 2 ASP A 785 OD1 105.6 REMARK 620 3 DC B 112 O3' 168.0 76.7 REMARK 620 4 XG4 A 901 O1A 102.5 93.4 89.0 REMARK 620 5 HOH A1044 O 90.9 100.6 77.1 157.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XG4 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 MN A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 302 DBREF 6FBI A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 6FBI B 101 112 PDB 6FBI 6FBI 101 112 DBREF 6FBI C 201 216 PDB 6FBI 6FBI 201 216 SEQADV 6FBI 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 DC DG DG DC DC DA DC SEQRES 1 C 16 DA DA DA DC DG DT DG DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC HET XG4 A 901 44 HET MN A 902 1 HET MN A 903 1 HET EDO A 904 10 HET EDO C 301 10 HET EDO C 302 10 HETNAM XG4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 XG4 PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 XG4 C10 H17 N6 O12 P3 FORMUL 5 MN 2(MN 2+) FORMUL 7 EDO 3(C2 H6 O2) FORMUL 10 HOH *209(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 PHE A 700 1 16 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 PHE A 306 O ALA A 327 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 577 N ARG A 563 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 GLU A 820 N ASP A 610 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 903 1555 1555 2.08 LINK OD2 ASP A 610 MN MN A 902 1555 1555 2.11 LINK O TYR A 611 MN MN A 903 1555 1555 2.18 LINK OD1 ASP A 785 MN MN A 902 1555 1555 1.80 LINK OD2 ASP A 785 MN MN A 903 1555 1555 1.97 LINK O3' DC B 112 MN MN A 902 1555 1555 2.27 LINK O1A XG4 A 901 MN MN A 903 1555 1555 2.19 LINK O1A XG4 A 901 MN MN A 902 1555 1555 2.21 LINK O1B XG4 A 901 MN MN A 903 1555 1555 1.96 LINK O3G XG4 A 901 MN MN A 903 1555 1555 2.18 LINK MN MN A 902 O HOH A1044 1555 1555 2.15 CISPEP 1 TRP A 299 PRO A 300 0 0.68 CISPEP 2 ASP A 578 PRO A 579 0 -1.52 SITE 1 AC1 21 ARG A 573 ASP A 610 TYR A 611 GLN A 613 SITE 2 AC1 21 ILE A 614 GLU A 615 HIS A 639 ARG A 659 SITE 3 AC1 21 ARG A 660 LYS A 663 PHE A 667 TYR A 671 SITE 4 AC1 21 ASP A 785 MN A 902 MN A 903 HOH A1001 SITE 5 AC1 21 HOH A1003 HOH A1042 DC B 112 DC C 204 SITE 6 AC1 21 DG C 205 SITE 1 AC2 7 ASP A 610 ASP A 785 XG4 A 901 MN A 903 SITE 2 AC2 7 HOH A1001 HOH A1044 DC B 112 SITE 1 AC3 5 ASP A 610 TYR A 611 ASP A 785 XG4 A 901 SITE 2 AC3 5 MN A 902 SITE 1 AC4 3 TRP A 417 ARG A 431 ARG A 435 SITE 1 AC5 3 DG C 207 DG C 208 HOH C 406 SITE 1 AC6 3 DG C 213 DG C 214 HOH C 426 CRYST1 109.770 109.770 91.460 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 0.009110 0.005260 0.000000 0.00000 SCALE2 0.000000 0.010519 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010934 0.00000