HEADER DNA BINDING PROTEIN/DNA 16-JUN-17 5W6K TITLE STRUCTURE OF MUTANT TAQ POLYMERASE INCORPORATING UNNATURAL BASE PAIRS TITLE 2 Z:P COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 293-831; COMPND 5 SYNONYM: TAQ POLYMERASE 1; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(P*(1WA)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-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: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 562; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 14 ORGANISM_TAXID: 562 KEYWDS MUTANT TAQ POLYMERASE, UNNATURAL BASE PAIRS, AEGIS, TERNARY COMPLEX, KEYWDS 2 KLENTAQ, BINARY COMPLEX, TRANSFERASE-DNA COMPLEX, DNA BINDING KEYWDS 3 PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR I.SINGH,M.M.GEORGIADIS REVDAT 3 04-OCT-23 5W6K 1 LINK REVDAT 2 19-SEP-18 5W6K 1 JRNL REVDAT 1 18-JUL-18 5W6K 0 JRNL AUTH I.SINGH,R.LAOS,S.HOSHIKA,S.A.BENNER,M.M.GEORGIADIS JRNL TITL SNAPSHOTS OF AN EVOLVED DNA POLYMERASE PRE- AND JRNL TITL 2 POST-INCORPORATION OF AN UNNATURAL NUCLEOTIDE. JRNL REF NUCLEIC ACIDS RES. V. 46 7977 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 29986111 JRNL DOI 10.1093/NAR/GKY552 REMARK 2 REMARK 2 RESOLUTION. 2.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 25878 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 1229 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 41.9847 - 4.8623 0.99 3000 106 0.1974 0.2390 REMARK 3 2 4.8623 - 3.8602 1.00 2866 131 0.1788 0.1966 REMARK 3 3 3.8602 - 3.3725 1.00 2824 149 0.2077 0.2519 REMARK 3 4 3.3725 - 3.0642 1.00 2846 136 0.2395 0.3194 REMARK 3 5 3.0642 - 2.8446 1.00 2762 188 0.2508 0.3075 REMARK 3 6 2.8446 - 2.6770 1.00 2785 155 0.2705 0.3216 REMARK 3 7 2.6770 - 2.5429 0.98 2778 132 0.2784 0.3479 REMARK 3 8 2.5429 - 2.4322 0.96 2726 116 0.2745 0.3343 REMARK 3 9 2.4322 - 2.3386 0.74 2062 116 0.2884 0.3478 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.72 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 : 0.003 4819 REMARK 3 ANGLE : 0.590 6635 REMARK 3 CHIRALITY : 0.039 734 REMARK 3 PLANARITY : 0.003 774 REMARK 3 DIHEDRAL : 14.448 2818 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 296 THROUGH 448 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.3858 -41.4522 -18.0278 REMARK 3 T TENSOR REMARK 3 T11: 0.2916 T22: 0.2177 REMARK 3 T33: 0.5514 T12: -0.0624 REMARK 3 T13: 0.1434 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 1.2741 L22: 0.8280 REMARK 3 L33: 0.8239 L12: 0.1154 REMARK 3 L13: 0.1061 L23: -0.0246 REMARK 3 S TENSOR REMARK 3 S11: -0.0904 S12: -0.0337 S13: -0.7241 REMARK 3 S21: -0.2608 S22: 0.0250 S23: -0.3765 REMARK 3 S31: 0.2145 S32: 0.0756 S33: 0.0627 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 449 THROUGH 604 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.9072 -11.0043 0.8575 REMARK 3 T TENSOR REMARK 3 T11: 0.6238 T22: 0.2008 REMARK 3 T33: 0.3284 T12: -0.0254 REMARK 3 T13: 0.1067 T23: -0.0224 REMARK 3 L TENSOR REMARK 3 L11: 0.4789 L22: 0.4973 REMARK 3 L33: 0.3864 L12: 0.4249 REMARK 3 L13: 0.0048 L23: -0.2043 REMARK 3 S TENSOR REMARK 3 S11: 0.1679 S12: -0.0827 S13: 0.2585 REMARK 3 S21: -0.0566 S22: -0.0597 S23: 0.0939 REMARK 3 S31: -0.8041 S32: -0.0549 S33: -0.0710 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 605 THROUGH 713 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.8414 -16.9606 -7.5362 REMARK 3 T TENSOR REMARK 3 T11: 0.5030 T22: 0.9817 REMARK 3 T33: 0.2947 T12: 0.4331 REMARK 3 T13: -0.0429 T23: 0.0937 REMARK 3 L TENSOR REMARK 3 L11: 0.3148 L22: 0.1219 REMARK 3 L33: 1.2375 L12: -0.0049 REMARK 3 L13: -0.2558 L23: -0.3438 REMARK 3 S TENSOR REMARK 3 S11: -0.1654 S12: -0.4167 S13: 0.1839 REMARK 3 S21: 0.1014 S22: 0.3053 S23: 0.2226 REMARK 3 S31: -0.6106 S32: -0.8399 S33: 0.3803 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 714 THROUGH 831 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9163 -25.6287 -16.6075 REMARK 3 T TENSOR REMARK 3 T11: 0.2827 T22: 0.4150 REMARK 3 T33: 0.2078 T12: 0.0245 REMARK 3 T13: 0.0002 T23: 0.0875 REMARK 3 L TENSOR REMARK 3 L11: 0.8946 L22: 0.7909 REMARK 3 L33: 1.4972 L12: 0.2926 REMARK 3 L13: -0.3958 L23: 0.2142 REMARK 3 S TENSOR REMARK 3 S11: -0.0963 S12: 0.0795 S13: -0.0530 REMARK 3 S21: -0.2659 S22: 0.2109 S23: 0.0684 REMARK 3 S31: -0.3383 S32: -0.7270 S33: -0.1193 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.5504 -29.9145 5.2064 REMARK 3 T TENSOR REMARK 3 T11: 0.2782 T22: 0.7179 REMARK 3 T33: 0.7612 T12: 0.1222 REMARK 3 T13: -0.1295 T23: 0.1533 REMARK 3 L TENSOR REMARK 3 L11: 5.2442 L22: 0.6000 REMARK 3 L33: 0.7979 L12: -1.5702 REMARK 3 L13: -0.1298 L23: 0.3602 REMARK 3 S TENSOR REMARK 3 S11: 0.0369 S12: 0.4578 S13: -0.1785 REMARK 3 S21: -0.0537 S22: -0.1049 S23: -0.0178 REMARK 3 S31: -0.0906 S32: -0.1026 S33: -0.0326 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 204 THROUGH 212 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.0410 -22.2727 0.8740 REMARK 3 T TENSOR REMARK 3 T11: 0.2084 T22: 0.2948 REMARK 3 T33: 0.1907 T12: 0.0877 REMARK 3 T13: 0.0334 T23: 0.0600 REMARK 3 L TENSOR REMARK 3 L11: 2.2877 L22: 1.4549 REMARK 3 L33: 0.9206 L12: 1.0383 REMARK 3 L13: 0.9157 L23: 0.6263 REMARK 3 S TENSOR REMARK 3 S11: -0.0249 S12: -0.2879 S13: 0.0101 REMARK 3 S21: 0.0947 S22: 0.0792 S23: 0.0473 REMARK 3 S31: -0.2210 S32: -0.2878 S33: -0.0897 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 105 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.0776 -19.3392 1.3978 REMARK 3 T TENSOR REMARK 3 T11: 0.3432 T22: 0.2838 REMARK 3 T33: 0.2144 T12: 0.1373 REMARK 3 T13: 0.0379 T23: 0.0601 REMARK 3 L TENSOR REMARK 3 L11: 1.3106 L22: 0.3370 REMARK 3 L33: 2.5611 L12: 0.0737 REMARK 3 L13: 1.5312 L23: -0.4190 REMARK 3 S TENSOR REMARK 3 S11: 0.0996 S12: 0.2420 S13: 0.0854 REMARK 3 S21: -0.1101 S22: -0.1032 S23: -0.0623 REMARK 3 S31: -0.3175 S32: -0.2186 S33: 0.0269 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 213 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.6825 -27.5259 14.4848 REMARK 3 T TENSOR REMARK 3 T11: 0.2698 T22: 0.4210 REMARK 3 T33: 0.4251 T12: 0.1844 REMARK 3 T13: -0.1637 T23: 0.0321 REMARK 3 L TENSOR REMARK 3 L11: 2.4730 L22: 2.5089 REMARK 3 L33: 0.3677 L12: -2.4027 REMARK 3 L13: 0.6702 L23: -0.8318 REMARK 3 S TENSOR REMARK 3 S11: -0.1991 S12: -0.2616 S13: 0.0588 REMARK 3 S21: 0.3562 S22: 0.2262 S23: 0.0248 REMARK 3 S31: -0.1215 S32: -0.1166 S33: 0.0204 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 5W6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1000227072. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26672 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.339 REMARK 200 RESOLUTION RANGE LOW (A) : 41.978 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3RTV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19 % PEG 4000, 0.2 M AMMONIUM ACETATE, REMARK 280 0.01 M MAGNESIUM ACETATE, 0.05 M SODIUM CACODYLATE PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277.16K 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 30.29033 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 60.58067 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 60.58067 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 30.29033 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: 5360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 A1133 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1137 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 293 REMARK 465 LEU A 294 REMARK 465 GLU A 295 REMARK 465 TYR A 686 REMARK 465 GLU A 687 REMARK 465 GLU A 688 REMARK 465 ALA A 689 REMARK 465 GLN A 690 REMARK 465 ALA A 691 REMARK 465 PHE A 692 REMARK 465 ILE A 693 REMARK 465 GLU A 694 REMARK 465 ARG A 695 REMARK 465 TYR A 696 REMARK 465 PHE A 697 REMARK 465 GLN A 698 REMARK 465 SER A 699 REMARK 465 VAL 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 462 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 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. = 1.9 DEGREES REMARK 500 DOC B 112 O3' - P - OP1 ANGL. DEV. = -28.9 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 328 103.85 -168.99 REMARK 500 VAL A 433 -71.17 -123.68 REMARK 500 TYR A 545 -58.57 -121.59 REMARK 500 VAL A 586 -22.52 -154.05 REMARK 500 ALA A 653 32.81 -85.96 REMARK 500 ALA A 683 65.45 63.83 REMARK 500 HIS A 784 -69.01 71.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1142 DISTANCE = 5.94 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 902 MG 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 78.9 89.5 REMARK 620 4 A5J A 901 O1A 94.3 164.9 77.8 REMARK 620 5 A5J A 901 O2B 171.3 106.2 92.4 82.6 REMARK 620 6 A5J A 901 O2G 89.0 98.9 163.2 91.6 99.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 903 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 ASP A 785 OD1 108.9 REMARK 620 3 A5J A 901 O1A 112.5 92.5 REMARK 620 4 HOH A1028 O 91.6 157.6 87.6 REMARK 620 5 HOH A1056 O 90.2 86.2 156.2 84.8 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 A5J A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 903 DBREF 5W6K A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 5W6K B 101 112 PDB 5W6K 5W6K 101 112 DBREF 5W6K C 204 216 PDB 5W6K 5W6K 204 216 SEQADV 5W6K VAL A 444 UNP P19821 MET 444 ENGINEERED MUTATION SEQADV 5W6K ALA A 527 UNP P19821 PRO 527 ENGINEERED MUTATION SEQADV 5W6K GLU A 551 UNP P19821 ASP 551 ENGINEERED MUTATION SEQADV 5W6K VAL A 832 UNP P19821 GLU 832 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 VAL GLU ALA THR GLY SEQRES 13 A 540 VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER LEU SEQRES 14 A 540 GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU VAL SEQRES 15 A 540 PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER ARG SEQRES 16 A 540 ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY LEU SEQRES 17 A 540 PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SER SEQRES 18 A 540 THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA HIS SEQRES 19 A 540 ALA 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 GLU LEU SEQRES 21 A 540 ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE ASN SEQRES 22 A 540 GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER ASP SEQRES 23 A 540 PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU GLY SEQRES 24 A 540 GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY TRP SEQRES 25 A 540 LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU ARG SEQRES 26 A 540 VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE ARG SEQRES 27 A 540 VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR ALA SEQRES 28 A 540 SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP PRO SEQRES 29 A 540 LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY VAL SEQRES 30 A 540 LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU LEU SEQRES 31 A 540 ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU ARG SEQRES 32 A 540 TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE GLU SEQRES 33 A 540 LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL GLU SEQRES 34 A 540 THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU GLU SEQRES 35 A 540 ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG MET SEQRES 36 A 540 ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP LEU SEQRES 37 A 540 MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU GLU SEQRES 38 A 540 GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP GLU SEQRES 39 A 540 LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA VAL SEQRES 40 A 540 ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR PRO SEQRES 41 A 540 LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY GLU SEQRES 42 A 540 ASP TRP LEU SER ALA LYS VAL SEQRES 1 B 12 DG DA DC DC DA DC DG DG DC DG DC DOC SEQRES 1 C 13 1WA DG DG DC DG DC DC DG DT DG DG DT DC HET DOC B 112 30 HET 1WA C 204 34 HET A5J A 901 45 HET MG A 902 1 HET MG A 903 1 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM 1WA 2-AMINO-8-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 1WA PENTOFURANOSYL)-4-HYDROXY-1H-IMIDAZO[1,2-A][1,3, HETNAM 3 1WA 5]TRIAZINE-5,8-DIIUM HETNAM A5J (1R)-1-[6-AMINO-5-(DIHYDROXYAMINO)-2-HYDROXYPYRIDIN-3- HETNAM 2 A5J YL]-1,4-ANHYDRO-2-DEOXY-5-O-[(S)-HYDROXY{[(S)- HETNAM 3 A5J HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-D- HETNAM 4 A5J ERYTHRO-PENTITOL HETNAM MG MAGNESIUM ION FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 3 1WA C10 H16 N5 O7 P 2+ FORMUL 4 A5J C10 H18 N3 O15 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *167(H2 O) HELIX 1 AA1 GLU A 337 LEU A 342 1 6 HELIX 2 AA2 ARG A 343 LEU A 345 5 3 HELIX 3 AA3 LEU A 352 GLU A 363 1 12 HELIX 4 AA4 ASP A 372 ASP A 381 1 10 HELIX 5 AA5 THR A 386 GLY A 395 1 10 HELIX 6 AA6 GLU A 401 LEU A 420 1 20 HELIX 7 AA7 GLU A 423 VAL A 433 1 11 HELIX 8 AA8 VAL A 433 GLY A 448 1 16 HELIX 9 AA9 ASP A 452 GLY A 479 1 28 HELIX 10 AB1 SER A 486 ASP A 496 1 11 HELIX 11 AB2 SER A 515 ALA A 521 1 7 HELIX 12 AB3 HIS A 526 TYR A 545 1 20 HELIX 13 AB4 PRO A 548 ILE A 553 5 6 HELIX 14 AB5 THR A 588 ARG A 596 1 9 HELIX 15 AB6 GLN A 613 GLY A 624 1 12 HELIX 16 AB7 ASP A 625 GLU A 634 1 10 HELIX 17 AB8 ASP A 637 PHE A 647 1 11 HELIX 18 AB9 ASP A 655 TYR A 671 1 17 HELIX 19 AC1 SER A 674 GLN A 680 1 7 HELIX 20 AC2 LYS A 702 GLY A 718 1 17 HELIX 21 AC3 PRO A 731 ALA A 735 5 5 HELIX 22 AC4 VAL A 737 MET A 775 1 39 HELIX 23 AC5 ARG A 795 GLY A 809 1 15 SHEET 1 AA1 3 PHE A 306 LEU A 311 0 SHEET 2 AA1 3 LEU A 321 ALA A 327 -1 O ALA A 327 N PHE A 306 SHEET 3 AA1 3 VAL A 332 ARG A 334 -1 O HIS A 333 N ALA A 326 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 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 O3' DC B 111 P DOC B 112 1555 1555 1.59 LINK O3' 1WA C 204 P DG C 205 1555 1555 1.59 LINK OD1 ASP A 610 MG MG A 902 1555 1555 2.23 LINK OD2 ASP A 610 MG MG A 903 1555 1555 2.15 LINK O TYR A 611 MG MG A 902 1555 1555 1.89 LINK OD2 ASP A 785 MG MG A 902 1555 1555 2.23 LINK OD1 ASP A 785 MG MG A 903 1555 1555 2.01 LINK O1A A5J A 901 MG MG A 902 1555 1555 2.21 LINK O2B A5J A 901 MG MG A 902 1555 1555 2.04 LINK O2G A5J A 901 MG MG A 902 1555 1555 2.11 LINK O1A A5J A 901 MG MG A 903 1555 1555 2.26 LINK MG MG A 903 O HOH A1028 1555 1555 2.64 LINK MG MG A 903 O HOH A1056 1555 1555 2.35 CISPEP 1 TRP A 299 PRO A 300 0 2.23 CISPEP 2 ASP A 578 PRO A 579 0 -4.96 SITE 1 AC1 22 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC1 22 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC1 22 ARG A 659 ARG A 660 LYS A 663 PHE A 667 SITE 4 AC1 22 ASP A 785 MG A 902 MG A 903 HOH A1023 SITE 5 AC1 22 HOH A1028 HOH A1040 HOH A1055 DOC B 112 SITE 6 AC1 22 1WA C 204 DG C 205 SITE 1 AC2 5 ASP A 610 TYR A 611 ASP A 785 A5J A 901 SITE 2 AC2 5 MG A 903 SITE 1 AC3 6 ASP A 610 ASP A 785 A5J A 901 MG A 902 SITE 2 AC3 6 HOH A1028 HOH A1056 CRYST1 109.306 109.306 90.871 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 0.009149 0.005282 0.000000 0.00000 SCALE2 0.000000 0.010564 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011005 0.00000