HEADER DNA BINDING PROTEIN 19-DEC-17 6FBH TITLE KLENTAQ DNA POLYMERASE PROCESSING A MODIFIED PRIMER - BEARING THE TITLE 2 MODIFICATION UPSTREAM AT THE SIXTH 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*CP*AP*(OH3)P*CP*GP*GP*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*CP*CP*GP*GP*TP*GP*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 6FBH 1 COMPND REMARK REVDAT 2 10-OCT-18 6FBH 1 COMPND JRNL REVDAT 1 26-SEP-18 6FBH 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.250 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 113873 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 5772 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 47.5206 - 5.5891 1.00 3598 206 0.1620 0.1744 REMARK 3 2 5.5891 - 4.4373 1.00 3621 183 0.1459 0.1688 REMARK 3 3 4.4373 - 3.8767 0.99 3552 214 0.1434 0.1883 REMARK 3 4 3.8767 - 3.5223 1.00 3584 228 0.1662 0.1823 REMARK 3 5 3.5223 - 3.2699 1.00 3603 189 0.1757 0.2180 REMARK 3 6 3.2699 - 3.0772 1.00 3617 194 0.1976 0.1934 REMARK 3 7 3.0772 - 2.9231 1.00 3582 192 0.1989 0.2137 REMARK 3 8 2.9231 - 2.7959 1.00 3578 209 0.2174 0.2768 REMARK 3 9 2.7959 - 2.6883 1.00 3617 191 0.2239 0.2200 REMARK 3 10 2.6883 - 2.5955 1.00 3595 200 0.2191 0.2892 REMARK 3 11 2.5955 - 2.5143 1.00 3643 210 0.2155 0.2480 REMARK 3 12 2.5143 - 2.4425 1.00 3594 183 0.2112 0.2463 REMARK 3 13 2.4425 - 2.3782 1.00 3592 150 0.2202 0.2522 REMARK 3 14 2.3782 - 2.3202 1.00 3659 179 0.2256 0.2598 REMARK 3 15 2.3202 - 2.2674 1.00 3529 208 0.2364 0.2676 REMARK 3 16 2.2674 - 2.2192 1.00 3698 147 0.2391 0.3231 REMARK 3 17 2.2192 - 2.1748 1.00 3611 187 0.2436 0.2844 REMARK 3 18 2.1748 - 2.1337 1.00 3649 163 0.2411 0.2505 REMARK 3 19 2.1337 - 2.0956 1.00 3623 194 0.2578 0.2925 REMARK 3 20 2.0956 - 2.0601 1.00 3602 185 0.2830 0.3126 REMARK 3 21 2.0601 - 2.0269 1.00 3577 187 0.2882 0.3085 REMARK 3 22 2.0269 - 1.9957 1.00 3613 219 0.2865 0.2971 REMARK 3 23 1.9957 - 1.9663 1.00 3601 200 0.2937 0.2982 REMARK 3 24 1.9663 - 1.9386 1.00 3609 182 0.3040 0.3355 REMARK 3 25 1.9386 - 1.9124 1.00 3627 208 0.3146 0.3525 REMARK 3 26 1.9124 - 1.8876 1.00 3580 174 0.3230 0.3827 REMARK 3 27 1.8876 - 1.8640 1.00 3604 197 0.3359 0.3593 REMARK 3 28 1.8640 - 1.8415 1.00 3579 226 0.3526 0.3888 REMARK 3 29 1.8415 - 1.8201 1.00 3594 203 0.3688 0.3788 REMARK 3 30 1.8201 - 1.7997 0.99 3570 164 0.3641 0.3648 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.750 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 : 0.009 4980 REMARK 3 ANGLE : 0.841 6867 REMARK 3 CHIRALITY : 0.047 766 REMARK 3 PLANARITY : 0.005 828 REMARK 3 DIHEDRAL : 17.100 2912 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): 39.8200 -42.7604 -17.9886 REMARK 3 T TENSOR REMARK 3 T11: 0.4302 T22: 0.4719 REMARK 3 T33: 0.9212 T12: -0.1607 REMARK 3 T13: 0.1472 T23: -0.1205 REMARK 3 L TENSOR REMARK 3 L11: 2.1883 L22: 1.6370 REMARK 3 L33: 2.1340 L12: -0.0780 REMARK 3 L13: 0.1757 L23: 0.2632 REMARK 3 S TENSOR REMARK 3 S11: -0.0484 S12: 0.1194 S13: -1.0667 REMARK 3 S21: -0.2039 S22: 0.0878 S23: -0.5237 REMARK 3 S31: 0.3865 S32: 0.0225 S33: -0.0356 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 434 THROUGH 633 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.3166 -13.9106 -3.6683 REMARK 3 T TENSOR REMARK 3 T11: 0.3924 T22: 0.2838 REMARK 3 T33: 0.3132 T12: 0.0863 REMARK 3 T13: 0.0310 T23: 0.0192 REMARK 3 L TENSOR REMARK 3 L11: 1.7604 L22: 1.4927 REMARK 3 L33: 3.3371 L12: 1.2605 REMARK 3 L13: -0.5488 L23: -0.4155 REMARK 3 S TENSOR REMARK 3 S11: 0.0635 S12: 0.0194 S13: 0.1160 REMARK 3 S21: 0.0129 S22: 0.0151 S23: -0.0373 REMARK 3 S31: -0.9195 S32: -0.3381 S33: 0.0283 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 634 THROUGH 700 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.8150 -11.5391 -1.8532 REMARK 3 T TENSOR REMARK 3 T11: 0.8403 T22: 1.1523 REMARK 3 T33: 0.5085 T12: 0.5235 REMARK 3 T13: 0.0638 T23: 0.1054 REMARK 3 L TENSOR REMARK 3 L11: 1.6277 L22: 2.5195 REMARK 3 L33: 1.9801 L12: 0.5516 REMARK 3 L13: -1.2546 L23: 1.2215 REMARK 3 S TENSOR REMARK 3 S11: -0.0703 S12: -0.2300 S13: 0.3091 REMARK 3 S21: 0.1982 S22: 0.3666 S23: 0.4697 REMARK 3 S31: -1.2911 S32: -1.3491 S33: -0.2358 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 701 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.1758 -26.1865 -15.0913 REMARK 3 T TENSOR REMARK 3 T11: 0.2833 T22: 0.6648 REMARK 3 T33: 0.3159 T12: -0.0118 REMARK 3 T13: 0.0107 T23: 0.0326 REMARK 3 L TENSOR REMARK 3 L11: 1.2159 L22: 1.5572 REMARK 3 L33: 3.7283 L12: 0.6817 REMARK 3 L13: -0.0270 L23: -0.6092 REMARK 3 S TENSOR REMARK 3 S11: -0.2534 S12: 0.2517 S13: -0.1706 REMARK 3 S21: -0.2940 S22: 0.3468 S23: -0.0040 REMARK 3 S31: -0.1538 S32: -1.1554 S33: -0.0707 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.8481 -23.4425 4.0479 REMARK 3 T TENSOR REMARK 3 T11: 0.3564 T22: 0.4144 REMARK 3 T33: 0.3620 T12: 0.0713 REMARK 3 T13: 0.0510 T23: 0.0168 REMARK 3 L TENSOR REMARK 3 L11: 7.6881 L22: 2.2513 REMARK 3 L33: 2.8449 L12: -0.2096 REMARK 3 L13: 1.5259 L23: -1.3513 REMARK 3 S TENSOR REMARK 3 S11: 0.1830 S12: 0.4678 S13: -0.5963 REMARK 3 S21: -0.2051 S22: -0.3963 S23: -0.1842 REMARK 3 S31: 0.0808 S32: 0.6422 S33: 0.1735 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 201 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.7566 -21.1088 7.1835 REMARK 3 T TENSOR REMARK 3 T11: 0.4340 T22: 0.8829 REMARK 3 T33: 0.4126 T12: 0.0646 REMARK 3 T13: -0.0326 T23: 0.0748 REMARK 3 L TENSOR REMARK 3 L11: 3.5439 L22: 9.0492 REMARK 3 L33: 4.0174 L12: -2.5794 REMARK 3 L13: -1.9709 L23: 2.8433 REMARK 3 S TENSOR REMARK 3 S11: -0.1697 S12: -0.2960 S13: 0.5829 REMARK 3 S21: 1.0046 S22: -0.4022 S23: -0.4703 REMARK 3 S31: -0.1657 S32: -0.8286 S33: 0.4749 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 206 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.7675 -24.2345 5.9800 REMARK 3 T TENSOR REMARK 3 T11: 0.2448 T22: 0.3451 REMARK 3 T33: 0.3503 T12: 0.0044 REMARK 3 T13: -0.0067 T23: 0.0812 REMARK 3 L TENSOR REMARK 3 L11: 2.1984 L22: 4.1465 REMARK 3 L33: 1.1715 L12: -0.3609 REMARK 3 L13: -1.5493 L23: -0.5463 REMARK 3 S TENSOR REMARK 3 S11: -0.3612 S12: -0.2295 S13: -0.3523 REMARK 3 S21: 0.3918 S22: 0.2854 S23: -0.4874 REMARK 3 S31: -0.2355 S32: -0.0044 S33: 0.0535 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 6FBH 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_1200007861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 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 : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00002 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 113900 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 47.504 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.140 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.02 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.670 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 (%): 45.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 29 % PEG 4000, 0.05 M TRIS, 20 MM REMARK 280 MANGANESE(II) CHLORIDE, 0.2 M AMMONIUM CHLORIDE, PH 7.0, 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 30.43067 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 60.86133 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 60.86133 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 30.43067 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: 6080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 A1199 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 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 424 CG CD OE1 OE2 REMARK 470 GLU A 465 CG CD OE1 OE2 REMARK 470 ARG A 469 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 492 CG CD NE CZ NH1 NH2 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 ARG A 556 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 630 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 631 CG1 CG2 REMARK 470 GLU A 652 CG CD OE1 OE2 REMARK 470 LEU A 657 CG CD1 CD2 REMARK 470 GLU A 687 CG CD OE1 OE2 REMARK 470 GLU A 694 CG CD OE1 OE2 REMARK 470 GLN A 698 CG CD OE1 NE2 REMARK 470 LYS A 702 CG CD CE NZ REMARK 470 GLU A 794 CG CD OE1 OE2 REMARK 470 ARG A 795 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 801 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 832 CG CD OE1 OE2 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 OD1 ASP A 320 HH TYR A 339 1.58 REMARK 500 O HOH A 1047 O HOH A 1178 2.10 REMARK 500 OE2 GLU A 473 NH2 ARG A 476 2.11 REMARK 500 O HOH C 317 O HOH C 330 2.12 REMARK 500 O HOH A 1156 O HOH A 1173 2.12 REMARK 500 OP2 DG C 210 O HOH C 301 2.17 REMARK 500 O HOH A 1041 O HOH A 1185 2.18 REMARK 500 O PHE A 632 O HOH A 1001 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC B 112 O3' DC B 112 C3' -0.046 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 D4B B 107 O3' - P - OP1 ANGL. DEV. = 12.5 DEGREES REMARK 500 DG B 109 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT C 206 O5' - P - OP2 ANGL. DEV. = -5.9 DEGREES REMARK 500 DG C 213 O4' - C1' - N9 ANGL. DEV. = 1.8 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 328 148.12 -174.54 REMARK 500 ASP A 381 107.36 -167.18 REMARK 500 THR A 399 -160.72 -105.26 REMARK 500 VAL A 433 -64.12 -127.40 REMARK 500 TYR A 545 -58.76 -126.00 REMARK 500 VAL A 586 -18.20 -153.58 REMARK 500 HIS A 784 -60.46 74.04 REMARK 500 TYR A 811 95.77 -167.38 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 74.7 REMARK 620 3 ASP A 785 OD2 94.0 90.0 REMARK 620 4 XG4 A 904 O1A 98.3 170.8 84.6 REMARK 620 5 XG4 A 904 O1B 170.9 100.3 93.6 87.5 REMARK 620 6 XG4 A 904 O3G 85.6 88.4 178.4 97.0 86.6 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 101.2 REMARK 620 3 DC B 112 O3' 164.8 73.6 REMARK 620 4 XG4 A 904 O1A 103.4 92.9 91.3 REMARK 620 5 HOH A1036 O 87.7 102.9 79.7 158.6 REMARK 620 6 HOH A1045 O 85.4 172.7 100.7 82.5 80.2 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 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 EDO A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XG4 A 904 DBREF 6FBH A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 6FBH B 101 112 PDB 6FBH 6FBH 101 112 DBREF 6FBH C 201 216 PDB 6FBH 6FBH 201 216 SEQADV 6FBH 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 DC DA D4B DC DG DG DA DC SEQRES 1 C 16 DA DA DA DC DG DT DC DC DG DG DT DG DG SEQRES 2 C 16 DG DT DC HET D4B B 107 44 HET MN A 901 1 HET MN A 902 1 HET EDO A 903 10 HET XG4 A 904 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 EDO 1,2-ETHANEDIOL HETNAM XG4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 XG4 PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 D4B C19 H18 N3 O7 P FORMUL 4 MN 2(MN 2+) FORMUL 6 EDO C2 H6 O2 FORMUL 7 XG4 C10 H17 N6 O12 P3 FORMUL 8 HOH *264(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 GLU A 295 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 2.16 LINK OD2 ASP A 610 MN MN A 901 1555 1555 2.20 LINK O TYR A 611 MN MN A 902 1555 1555 2.18 LINK OD1 ASP A 785 MN MN A 901 1555 1555 2.06 LINK OD2 ASP A 785 MN MN A 902 1555 1555 2.13 LINK O3' DA B 106 P D4B B 107 1555 1555 1.58 LINK O3' D4B B 107 P DC B 108 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 904 1555 1555 2.15 LINK MN MN A 901 O HOH A1036 1555 1555 2.07 LINK MN MN A 901 O HOH A1045 1555 1555 1.81 LINK MN MN A 902 O1A XG4 A 904 1555 1555 2.32 LINK MN MN A 902 O1B XG4 A 904 1555 1555 2.19 LINK MN MN A 902 O3G XG4 A 904 1555 1555 2.01 CISPEP 1 TRP A 299 PRO A 300 0 4.44 CISPEP 2 ASP A 578 PRO A 579 0 3.01 SITE 1 AC1 7 ASP A 610 ASP A 785 MN A 902 XG4 A 904 SITE 2 AC1 7 HOH A1036 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 904 SITE 1 AC3 6 ARG A 313 TRP A 318 LEU A 552 HOH A1046 SITE 2 AC3 6 HOH A1073 HOH A1143 SITE 1 AC4 22 ARG A 573 ASP A 610 TYR A 611 GLN A 613 SITE 2 AC4 22 ILE A 614 GLU A 615 HIS A 639 ARG A 659 SITE 3 AC4 22 ARG A 660 LYS A 663 PHE A 667 TYR A 671 SITE 4 AC4 22 ASP A 785 MN A 901 MN A 902 HOH A1045 SITE 5 AC4 22 HOH A1101 HOH A1128 DC B 112 HOH B 207 SITE 6 AC4 22 DC C 204 DG C 205 CRYST1 109.706 109.706 91.292 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 0.009115 0.005263 0.000000 0.00000 SCALE2 0.000000 0.010525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010954 0.00000