HEADER TRANSFERASE/RNA 30-OCT-14 4WTG TITLE CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G E86Q TITLE 2 E87Q C223H V321I MUTATIONS AND DELTA8 BETA HAIRPIN LOOP DELETION IN TITLE 3 COMPLEX WITH SOFOSBUVIR DIPHOSPHATE GS-607596, MN2+ AND SYMMETRICAL TITLE 4 PRIMER TEMPLATE 5'-CAAAAUUU COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA PRIMER TEMPLATE CAAAAUUU; COMPND 3 CHAIN: T, P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA-DIRECTED RNA POLYMERASE; COMPND 7 CHAIN: A; COMPND 8 EC: 2.7.7.48; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS JFH-1; SOURCE 7 ORGANISM_TAXID: 356411; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HCV, VIRAL, NS5B, RDRP, RESISTANCE MUTATION, TEMPLATE, PRIMER, PRIMED KEYWDS 2 INITIATION, DELTA8 BETA HAIRPIN LOOP DELETION, TRANSFERASE-RNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.E.EDWARDS,T.C.APPLEBY REVDAT 3 27-SEP-17 4WTG 1 SOURCE JRNL REMARK REVDAT 2 25-FEB-15 4WTG 1 JRNL REVDAT 1 11-FEB-15 4WTG 0 JRNL AUTH T.C.APPLEBY,J.K.PERRY,E.MURAKAMI,O.BARAUSKAS,J.FENG,A.CHO, JRNL AUTH 2 D.FOX,D.R.WETMORE,M.E.MCGRATH,A.S.RAY,M.J.SOFIA, JRNL AUTH 3 S.SWAMINATHAN,T.E.EDWARDS JRNL TITL STRUCTURAL BASIS FOR RNA REPLICATION BY THE HEPATITIS C JRNL TITL 2 VIRUS POLYMERASE. JRNL REF SCIENCE V. 347 771 2015 JRNL REFN ESSN 1095-9203 JRNL PMID 25678663 JRNL DOI 10.1126/SCIENCE.1259210 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 22607 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1074 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1579 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.3430 REMARK 3 BIN FREE R VALUE SET COUNT : 88 REMARK 3 BIN FREE R VALUE : 0.4280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4073 REMARK 3 NUCLEIC ACID ATOMS : 254 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.89000 REMARK 3 B22 (A**2) : 1.89000 REMARK 3 B33 (A**2) : -6.14000 REMARK 3 B12 (A**2) : 0.95000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.565 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.311 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.243 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.740 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4477 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4037 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6163 ; 1.480 ; 1.926 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9290 ; 0.817 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 534 ; 6.334 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;35.582 ;22.439 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 655 ;16.876 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;16.360 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 703 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4856 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 996 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2139 ; 3.263 ; 5.602 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2138 ; 3.254 ; 5.601 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2672 ; 5.112 ; 8.402 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4WTG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000204483. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22607 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.67500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4OBC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NS5B AT 5.1 MG/ML IN 5 MM TRIS PH 7.5, REMARK 280 200 MM NH4OAC, 1 MM EDTA, 1 MM DTT AGAINST 25% PEG 550MME, 50 MM REMARK 280 MGCL2, 0.1 M HEPES PH 7.5 FOR CRYSTAL GROWTH SOAKED, INTO 28% REMARK 280 PEG 550 MME, 0.2 M AMMONIUM ACETATE, 0.05 M BISTRIS PROPANE PH REMARK 280 6.0, 0.05 M TRIS PH 7.2, 12 MM MNCL2, 20 MM GS-607596, 4 MM 5'- REMARK 280 CAAAAUUU WITH 8% GLYCEROL AS CRYO-PROTECTANT, CRYSTAL TRACKING REMARK 280 ID 251148C4, UNIQUE PUCK ID MCI3-1, PH 6.6, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 61.08000 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 30.54000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.81000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 15.27000 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 76.35000 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 APPLY THE FOLLOWING TO CHAINS: T, P, A 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 C P -1 REMARK 465 A P 0 REMARK 465 MET A -1 REMARK 465 ARG A 543 REMARK 465 LEU A 544 REMARK 465 LEU A 545 REMARK 465 ASP A 546 REMARK 465 LEU A 547 REMARK 465 SER A 548 REMARK 465 SER A 549 REMARK 465 TRP A 550 REMARK 465 PHE A 551 REMARK 465 THR A 552 REMARK 465 VAL A 553 REMARK 465 GLY A 554 REMARK 465 ALA A 555 REMARK 465 GLY A 556 REMARK 465 GLY A 557 REMARK 465 GLY A 558 REMARK 465 ASP A 559 REMARK 465 ILE A 560 REMARK 465 PHE A 561 REMARK 465 HIS A 562 REMARK 465 SER A 563 REMARK 465 VAL A 564 REMARK 465 SER A 565 REMARK 465 ARG A 566 REMARK 465 ALA A 567 REMARK 465 ARG A 568 REMARK 465 PRO A 569 REMARK 465 ARG A 570 REMARK 465 LEU A 571 REMARK 465 GLU A 572 REMARK 465 HIS A 573 REMARK 465 HIS A 574 REMARK 465 HIS A 575 REMARK 465 HIS A 576 REMARK 465 HIS A 577 REMARK 465 HIS A 578 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 C T 1 O5' C5' C4' O4' C3' C2' O2' REMARK 470 C T 1 C1' N1 C2 O2 N3 C4 N4 REMARK 470 C T 1 C5 C6 REMARK 470 A P 1 P OP1 OP2 O5' C5' C4' O4' REMARK 470 A P 1 C3' C2' O2' C1' N9 C8 N7 REMARK 470 A P 1 C5 C6 N6 N1 C2 N3 C4 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 50 CG CD CE NZ REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 LEU A 73 CG CD1 CD2 REMARK 470 LYS A 106 CG CD CE NZ REMARK 470 LYS A 124 CG CD CE NZ REMARK 470 LYS A 151 CG CD CE NZ REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 LYS A 212 CG CD CE NZ REMARK 470 LYS A 270 CG CD CE NZ REMARK 470 GLU A 330 CG CD OE1 OE2 REMARK 470 ARG A 377 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 379 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 401 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 440 CG OD1 OD2 REMARK 470 GLN A 441 CG CD OE1 NE2 REMARK 470 ASN A 442 CG OD1 ND2 REMARK 470 ARG A 465 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 501 CG CD CE NZ REMARK 470 LYS A 531 CG CD CE NZ REMARK 470 THR A 532 OG1 CG2 REMARK 470 LYS A 533 CG CD CE NZ REMARK 470 LYS A 535 CG CD CE NZ 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 ARG A 277 NE - CZ - NH2 ANGL. DEV. = -3.1 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 CYS A 14 56.35 -101.87 REMARK 500 TYR A 101 42.20 -93.44 REMARK 500 GLN A 131 -37.64 -138.38 REMARK 500 LYS A 151 48.90 -98.62 REMARK 500 ASP A 213 81.03 -151.67 REMARK 500 ALA A 242 -6.75 -52.75 REMARK 500 LEU A 260 -56.56 -125.07 REMARK 500 ALA A 348 69.57 -152.02 REMARK 500 VAL A 424 -66.77 -90.99 REMARK 500 LYS A 533 179.47 -59.03 REMARK 500 PRO A 540 -35.34 -31.70 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 P 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U P 6 O3' REMARK 620 2 ASP A 220 OD1 147.6 REMARK 620 3 ASP A 318 OD1 71.1 82.8 REMARK 620 4 ASP A 319 OD1 58.9 95.0 71.0 REMARK 620 5 HOH P 701 O 101.9 103.3 172.9 104.4 REMARK 620 6 6GS P 602 O2A 104.8 96.8 96.6 161.6 86.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 220 OD2 REMARK 620 2 THR A 221 O 83.6 REMARK 620 3 ASP A 318 OD2 94.5 84.7 REMARK 620 4 6GS P 602 O2A 98.9 176.4 97.6 REMARK 620 5 6GS P 602 O2B 160.6 90.0 103.2 86.8 REMARK 620 6 HOH P 702 O 83.5 84.3 169.0 93.4 77.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 237 OE2 REMARK 620 2 HIS A 254 ND1 85.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN P 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6GS P 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 603 DBREF 4WTG T 1 8 PDB 4WTG 4WTG 1 8 DBREF 4WTG P -1 6 PDB 4WTG 4WTG 1 8 DBREF 4WTG A 1 570 UNP Q99IB8 POLG_HCVJF 2443 3012 SEQADV 4WTG MET A -1 UNP Q99IB8 EXPRESSION TAG SEQADV 4WTG SER A 0 UNP Q99IB8 EXPRESSION TAG SEQADV 4WTG GLY A 15 UNP Q99IB8 SER 2457 ENGINEERED MUTATION SEQADV 4WTG GLN A 86 UNP Q99IB8 GLU 2528 ENGINEERED MUTATION SEQADV 4WTG GLN A 87 UNP Q99IB8 GLU 2529 ENGINEERED MUTATION SEQADV 4WTG HIS A 223 UNP Q99IB8 CYS 2665 ENGINEERED MUTATION SEQADV 4WTG ILE A 321 UNP Q99IB8 VAL 2763 ENGINEERED MUTATION SEQADV 4WTG A UNP Q99IB8 ASN 2886 DELETION SEQADV 4WTG A UNP Q99IB8 PHE 2887 DELETION SEQADV 4WTG A UNP Q99IB8 GLU 2888 DELETION SEQADV 4WTG A UNP Q99IB8 MET 2889 DELETION SEQADV 4WTG A UNP Q99IB8 TYR 2890 DELETION SEQADV 4WTG A UNP Q99IB8 GLY 2891 DELETION SEQADV 4WTG A UNP Q99IB8 SER 2892 DELETION SEQADV 4WTG A UNP Q99IB8 VAL 2893 DELETION SEQADV 4WTG GLY A 444 UNP Q99IB8 TYR 2894 LINKER SEQADV 4WTG GLY A 445 UNP Q99IB8 SER 2895 LINKER SEQADV 4WTG LEU A 571 UNP Q99IB8 EXPRESSION TAG SEQADV 4WTG GLU A 572 UNP Q99IB8 EXPRESSION TAG SEQADV 4WTG HIS A 573 UNP Q99IB8 EXPRESSION TAG SEQADV 4WTG HIS A 574 UNP Q99IB8 EXPRESSION TAG SEQADV 4WTG HIS A 575 UNP Q99IB8 EXPRESSION TAG SEQADV 4WTG HIS A 576 UNP Q99IB8 EXPRESSION TAG SEQADV 4WTG HIS A 577 UNP Q99IB8 EXPRESSION TAG SEQADV 4WTG HIS A 578 UNP Q99IB8 EXPRESSION TAG SEQRES 1 T 8 C A A A A U U U SEQRES 1 P 8 C A A A A U U U SEQRES 1 A 572 MET SER SER MET SER TYR SER TRP THR GLY ALA LEU ILE SEQRES 2 A 572 THR PRO CYS GLY PRO GLU GLU GLU LYS LEU PRO ILE ASN SEQRES 3 A 572 PRO LEU SER ASN SER LEU LEU ARG TYR HIS ASN LYS VAL SEQRES 4 A 572 TYR CYS THR THR SER LYS SER ALA SER GLN ARG ALA LYS SEQRES 5 A 572 LYS VAL THR PHE ASP ARG THR GLN VAL LEU ASP ALA HIS SEQRES 6 A 572 TYR ASP SER VAL LEU LYS ASP ILE LYS LEU ALA ALA SER SEQRES 7 A 572 LYS VAL SER ALA ARG LEU LEU THR LEU GLN GLN ALA CYS SEQRES 8 A 572 GLN LEU THR PRO PRO HIS SER ALA ARG SER LYS TYR GLY SEQRES 9 A 572 PHE GLY ALA LYS GLU VAL ARG SER LEU SER GLY ARG ALA SEQRES 10 A 572 VAL ASN HIS ILE LYS SER VAL TRP LYS ASP LEU LEU GLU SEQRES 11 A 572 ASP PRO GLN THR PRO ILE PRO THR THR ILE MET ALA LYS SEQRES 12 A 572 ASN GLU VAL PHE CYS VAL ASP PRO ALA LYS GLY GLY LYS SEQRES 13 A 572 LYS PRO ALA ARG LEU ILE VAL TYR PRO ASP LEU GLY VAL SEQRES 14 A 572 ARG VAL CYS GLU LYS MET ALA LEU TYR ASP ILE THR GLN SEQRES 15 A 572 LYS LEU PRO GLN ALA VAL MET GLY ALA SER TYR GLY PHE SEQRES 16 A 572 GLN TYR SER PRO ALA GLN ARG VAL GLU TYR LEU LEU LYS SEQRES 17 A 572 ALA TRP ALA GLU LYS LYS ASP PRO MET GLY PHE SER TYR SEQRES 18 A 572 ASP THR ARG HIS PHE ASP SER THR VAL THR GLU ARG ASP SEQRES 19 A 572 ILE ARG THR GLU GLU SER ILE TYR GLN ALA CYS SER LEU SEQRES 20 A 572 PRO GLU GLU ALA ARG THR ALA ILE HIS SER LEU THR GLU SEQRES 21 A 572 ARG LEU TYR VAL GLY GLY PRO MET PHE ASN SER LYS GLY SEQRES 22 A 572 GLN THR CYS GLY TYR ARG ARG CYS ARG ALA SER GLY VAL SEQRES 23 A 572 LEU THR THR SER MET GLY ASN THR ILE THR CYS TYR VAL SEQRES 24 A 572 LYS ALA LEU ALA ALA CYS LYS ALA ALA GLY ILE VAL ALA SEQRES 25 A 572 PRO THR MET LEU VAL CYS GLY ASP ASP LEU ILE VAL ILE SEQRES 26 A 572 SER GLU SER GLN GLY THR GLU GLU ASP GLU ARG ASN LEU SEQRES 27 A 572 ARG ALA PHE THR GLU ALA MET THR ARG TYR SER ALA PRO SEQRES 28 A 572 PRO GLY ASP PRO PRO ARG PRO GLU TYR ASP LEU GLU LEU SEQRES 29 A 572 ILE THR SER CYS SER SER ASN VAL SER VAL ALA LEU GLY SEQRES 30 A 572 PRO ARG GLY ARG ARG ARG TYR TYR LEU THR ARG ASP PRO SEQRES 31 A 572 THR THR PRO LEU ALA ARG ALA ALA TRP GLU THR VAL ARG SEQRES 32 A 572 HIS SER PRO ILE ASN SER TRP LEU GLY ASN ILE ILE GLN SEQRES 33 A 572 TYR ALA PRO THR ILE TRP VAL ARG MET VAL LEU MET THR SEQRES 34 A 572 HIS PHE PHE SER ILE LEU MET VAL GLN ASP THR LEU ASP SEQRES 35 A 572 GLN ASN LEU GLY GLY VAL ASN PRO LEU ASP LEU PRO ALA SEQRES 36 A 572 ILE ILE GLU ARG LEU HIS GLY LEU ASP ALA PHE SER MET SEQRES 37 A 572 HIS THR TYR SER HIS HIS GLU LEU THR ARG VAL ALA SER SEQRES 38 A 572 ALA LEU ARG LYS LEU GLY ALA PRO PRO LEU ARG VAL TRP SEQRES 39 A 572 LYS SER ARG ALA ARG ALA VAL ARG ALA SER LEU ILE SER SEQRES 40 A 572 ARG GLY GLY LYS ALA ALA VAL CYS GLY ARG TYR LEU PHE SEQRES 41 A 572 ASN TRP ALA VAL LYS THR LYS LEU LYS LEU THR PRO LEU SEQRES 42 A 572 PRO GLU ALA ARG LEU LEU ASP LEU SER SER TRP PHE THR SEQRES 43 A 572 VAL GLY ALA GLY GLY GLY ASP ILE PHE HIS SER VAL SER SEQRES 44 A 572 ARG ALA ARG PRO ARG LEU GLU HIS HIS HIS HIS HIS HIS HET MN P 601 1 HET 6GS P 602 26 HET MN A 601 1 HET MN A 602 1 HET CL A 603 1 HETNAM MN MANGANESE (II) ION HETNAM 6GS 2'-DEOXY-2'-FLUORO-2'-METHYLURIDINE 5'-(TRIHYDROGEN HETNAM 2 6GS DIPHOSPHATE) HETNAM CL CHLORIDE ION FORMUL 4 MN 3(MN 2+) FORMUL 5 6GS C10 H15 F N2 O11 P2 FORMUL 8 CL CL 1- FORMUL 9 HOH *59(H2 O) HELIX 1 AA1 TYR A 33 ASN A 35 5 3 HELIX 2 AA2 SER A 44 THR A 53 1 10 HELIX 3 AA3 ASP A 61 SER A 76 1 16 HELIX 4 AA4 THR A 84 THR A 92 1 9 HELIX 5 AA5 GLY A 104 SER A 110 1 7 HELIX 6 AA6 SER A 112 ASP A 129 1 18 HELIX 7 AA7 ASP A 164 GLY A 188 1 25 HELIX 8 AA8 ALA A 189 TYR A 195 5 7 HELIX 9 AA9 SER A 196 LYS A 211 1 16 HELIX 10 AB1 HIS A 223 VAL A 228 1 6 HELIX 11 AB2 THR A 229 ALA A 242 1 14 HELIX 12 AB3 PRO A 246 LEU A 260 1 15 HELIX 13 AB4 THR A 286 GLY A 307 1 22 HELIX 14 AB5 GLN A 327 TYR A 346 1 20 HELIX 15 AB6 ASP A 359 ILE A 363 5 5 HELIX 16 AB7 PRO A 388 ALA A 396 1 9 HELIX 17 AB8 PRO A 404 TYR A 415 1 12 HELIX 18 AB9 THR A 418 VAL A 424 1 7 HELIX 19 AC1 VAL A 424 ASP A 437 1 14 HELIX 20 AC2 ASN A 455 LEU A 457 5 3 HELIX 21 AC3 ASP A 458 GLY A 468 1 11 HELIX 22 AC4 LEU A 469 SER A 473 5 5 HELIX 23 AC5 SER A 478 GLY A 493 1 16 HELIX 24 AC6 PRO A 496 ARG A 514 1 19 HELIX 25 AC7 GLY A 516 PHE A 526 1 11 HELIX 26 AC8 ASN A 527 VAL A 530 5 4 SHEET 1 AA1 5 TYR A 4 TRP A 6 0 SHEET 2 AA1 5 THR A 273 ARG A 277 -1 O TYR A 276 N SER A 5 SHEET 3 AA1 5 GLY A 264 PHE A 267 -1 N MET A 266 O CYS A 274 SHEET 4 AA1 5 THR A 136 ALA A 140 1 N ILE A 138 O PHE A 267 SHEET 5 AA1 5 LEU A 159 TYR A 162 -1 O ILE A 160 N MET A 139 SHEET 1 AA2 2 VAL A 37 CYS A 39 0 SHEET 2 AA2 2 VAL A 144 CYS A 146 -1 O PHE A 145 N TYR A 38 SHEET 1 AA3 3 PRO A 214 TYR A 219 0 SHEET 2 AA3 3 ASP A 319 GLU A 325 -1 O SER A 324 N MET A 215 SHEET 3 AA3 3 VAL A 309 CYS A 316 -1 N CYS A 316 O ASP A 319 SHEET 1 AA4 2 ASN A 369 LEU A 374 0 SHEET 2 AA4 2 ARG A 380 THR A 385 -1 O ARG A 381 N ALA A 373 LINK O3' U P 6 MN MN P 601 1555 1555 2.37 LINK OD1 ASP A 220 MN MN P 601 1555 1555 2.16 LINK OD2 ASP A 220 MN MN A 601 1555 1555 2.20 LINK O THR A 221 MN MN A 601 1555 1555 2.19 LINK OE2 GLU A 237 MN MN A 602 1555 1555 2.14 LINK ND1 HIS A 254 MN MN A 602 1555 1555 2.21 LINK OD1 ASP A 318 MN MN P 601 1555 1555 2.13 LINK OD2 ASP A 318 MN MN A 601 1555 1555 2.08 LINK OD1 ASP A 319 MN MN P 601 1555 1555 2.16 LINK MN MN P 601 O HOH P 701 1555 1555 2.53 LINK MN MN P 601 O2A 6GS P 602 1555 1555 2.08 LINK O2A 6GS P 602 MN MN A 601 1555 1555 2.09 LINK O2B 6GS P 602 MN MN A 601 1555 1555 2.07 LINK MN MN A 601 O HOH P 702 1555 1555 2.54 SITE 1 AC1 7 ASP A 220 ASP A 318 ASP A 319 MN A 601 SITE 2 AC1 7 U P 6 6GS P 602 HOH P 701 SITE 1 AC2 18 ARG A 48 LYS A 141 ARG A 158 ASP A 220 SITE 2 AC2 18 THR A 221 HIS A 223 PHE A 224 ASP A 225 SITE 3 AC2 18 THR A 287 ASN A 291 ASP A 318 MN A 601 SITE 4 AC2 18 U P 6 MN P 601 HOH P 701 HOH P 702 SITE 5 AC2 18 A T 2 A T 3 SITE 1 AC3 6 ASP A 220 THR A 221 ASP A 318 MN P 601 SITE 2 AC3 6 6GS P 602 HOH P 702 SITE 1 AC4 2 GLU A 237 HIS A 254 SITE 1 AC5 6 GLY A 375 PRO A 376 ARG A 377 GLY A 378 SITE 2 AC5 6 ARG A 379 ARG A 381 CRYST1 140.440 140.440 91.620 90.00 90.00 120.00 P 65 12 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 0.007120 0.004111 0.000000 0.00000 SCALE2 0.000000 0.008222 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010915 0.00000 MASTER 430 0 5 26 12 0 12 6 0 0 0 46 END