HEADER VIRAL PROTEIN, TRANSFERASE 16-MAR-12 4E76 TITLE APO CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH BETA TITLE 2 HAIRPIN LOOP DELETION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-DIRECTED RNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEE REMARK 999; COMPND 5 SYNONYM: NS5B, P68; COMPND 6 EC: 2.7.7.48; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS; SOURCE 3 ORGANISM_COMMON: HCV; SOURCE 4 ORGANISM_TAXID: 356411; SOURCE 5 STRAIN: JFH-1; SOURCE 6 GENE: NS5B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: VCID 5854 KEYWDS RDRP, LOOPLESS DELTA8, FLAVIVIRIDAE, HEPATITIS C VIRUS, VIRAL KEYWDS 2 PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.E.EDWARDS,R.T.MOSLEY REVDAT 5 13-SEP-23 4E76 1 REMARK SEQADV REVDAT 4 26-JUL-17 4E76 1 SOURCE REMARK REVDAT 3 06-JUN-12 4E76 1 JRNL REVDAT 2 25-APR-12 4E76 1 JRNL REVDAT 1 18-APR-12 4E76 0 JRNL AUTH R.T.MOSLEY,T.E.EDWARDS,E.MURAKAMI,A.M.LAM,R.L.GRICE,J.DU, JRNL AUTH 2 M.J.SOFIA,P.A.FURMAN,M.J.OTTO JRNL TITL STRUCTURE OF HEPATITIS C VIRUS POLYMERASE IN COMPLEX WITH JRNL TITL 2 PRIMER-TEMPLATE RNA. JRNL REF J.VIROL. V. 86 6503 2012 JRNL REFN ISSN 0022-538X JRNL PMID 22496223 JRNL DOI 10.1128/JVI.00386-12 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 34323 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1731 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2266 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.4110 REMARK 3 BIN FREE R VALUE SET COUNT : 115 REMARK 3 BIN FREE R VALUE : 0.4630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4165 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.82000 REMARK 3 B22 (A**2) : 1.82000 REMARK 3 B33 (A**2) : -2.73000 REMARK 3 B12 (A**2) : 0.91000 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): 0.297 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.244 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.191 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.290 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 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): 4293 ; 0.012 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5853 ; 1.654 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 543 ; 6.701 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 168 ;35.164 ;22.321 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 680 ;17.545 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;18.994 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 672 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3220 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 19 REMARK 3 ORIGIN FOR THE GROUP (A): 32.7784 -31.8647 9.2850 REMARK 3 T TENSOR REMARK 3 T11: 0.0774 T22: 0.2563 REMARK 3 T33: 0.2431 T12: 0.0603 REMARK 3 T13: 0.0623 T23: 0.1316 REMARK 3 L TENSOR REMARK 3 L11: 4.1103 L22: 1.0748 REMARK 3 L33: 5.0506 L12: 0.2697 REMARK 3 L13: -1.0744 L23: -0.7299 REMARK 3 S TENSOR REMARK 3 S11: 0.3850 S12: -0.1140 S13: 0.5999 REMARK 3 S21: -0.0320 S22: -0.0239 S23: 0.1787 REMARK 3 S31: -0.4229 S32: -0.4976 S33: -0.3611 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 20 A 298 REMARK 3 ORIGIN FOR THE GROUP (A): 34.5790 -49.5801 8.0625 REMARK 3 T TENSOR REMARK 3 T11: 0.1127 T22: 0.3349 REMARK 3 T33: 0.1422 T12: -0.0646 REMARK 3 T13: -0.0453 T23: 0.0772 REMARK 3 L TENSOR REMARK 3 L11: 0.7032 L22: 0.1424 REMARK 3 L33: 0.8335 L12: 0.2690 REMARK 3 L13: -0.2210 L23: 0.0103 REMARK 3 S TENSOR REMARK 3 S11: -0.0247 S12: 0.2115 S13: 0.1238 REMARK 3 S21: 0.0423 S22: 0.0647 S23: 0.0089 REMARK 3 S31: 0.0783 S32: -0.2979 S33: -0.0400 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 299 A 367 REMARK 3 ORIGIN FOR THE GROUP (A): 50.3374 -53.0508 -9.9332 REMARK 3 T TENSOR REMARK 3 T11: 0.1622 T22: 0.3045 REMARK 3 T33: 0.1113 T12: -0.1164 REMARK 3 T13: -0.0337 T23: 0.0401 REMARK 3 L TENSOR REMARK 3 L11: 3.9624 L22: 1.5035 REMARK 3 L33: 0.9291 L12: -0.5705 REMARK 3 L13: 0.8204 L23: 0.2657 REMARK 3 S TENSOR REMARK 3 S11: -0.1862 S12: 0.3109 S13: 0.1191 REMARK 3 S21: 0.0693 S22: 0.1976 S23: -0.1768 REMARK 3 S31: 0.0082 S32: -0.1759 S33: -0.0114 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 368 A 543 REMARK 3 ORIGIN FOR THE GROUP (A): 63.4452 -52.5308 20.8222 REMARK 3 T TENSOR REMARK 3 T11: 0.2065 T22: 0.1747 REMARK 3 T33: 0.1684 T12: -0.0323 REMARK 3 T13: -0.0414 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.3245 L22: 1.0103 REMARK 3 L33: 1.2005 L12: -0.3140 REMARK 3 L13: -0.1316 L23: 0.3840 REMARK 3 S TENSOR REMARK 3 S11: 0.0133 S12: 0.0387 S13: -0.0010 REMARK 3 S21: 0.0660 S22: 0.0492 S23: 0.0190 REMARK 3 S31: 0.1950 S32: -0.0101 S33: -0.0625 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: U VALUES : WITH TLS ADDED REMARK 3 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 4 REMARK 4 4E76 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97650 REMARK 200 MONOCHROMATOR : ASYMMETRIC CURVED CRYSTAL REMARK 200 SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34324 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 94.8 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.67500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.320 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: PDB ENTRY 3I5K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.95 MG/ML NS5B IN 20 MM TRIS, PH 8, REMARK 280 200 MM SODIUM CHLORIDE, 20% GLYCEROL, 2 MM TCEP, 200 MM REMARK 280 IMIDAZOLE AGAINST 30% PEG550 MME, 0.1 M BIS-TRIS PROPANE, PH 6.5, REMARK 280 50 MM AMMONIUM SULFATE, CRYOPROTECTANT: 25% ETHYLENE GLYCOL, REMARK 280 CRYSTAL TRACKING ID 227386E9, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K, PH 6.9 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 61.75333 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 30.87667 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 46.31500 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 15.43833 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 77.19167 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A -1 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 SER A 15 OG REMARK 470 GLU A 19 CG CD OE1 OE2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 LYS A 106 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 ARG A 222 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 270 CG CD CE NZ REMARK 470 GLU A 333 CG CD OE1 OE2 REMARK 470 CYS A 366 SG REMARK 470 ARG A 401 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 441 CG CD OE1 NE2 REMARK 470 LYS A 531 CG CD CE NZ REMARK 470 LYS A 535 CG CD CE NZ REMARK 470 GLU A 541 CG CD OE1 OE2 REMARK 470 ARG A 543 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 544 CG CD1 CD2 REMARK 470 SER A 548 OG 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 TRP A 208 CE2 TRP A 208 CD2 0.076 REMARK 500 HIS A 428 CG HIS A 428 CD2 0.057 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 -103.30 -89.39 REMARK 500 GLU A 17 136.26 -36.83 REMARK 500 ARG A 98 172.63 -54.86 REMARK 500 TYR A 101 48.43 -108.63 REMARK 500 GLN A 131 -44.68 -132.96 REMARK 500 ALA A 150 -70.03 -26.23 REMARK 500 LYS A 151 47.67 -89.12 REMARK 500 CYS A 223 45.96 -100.49 REMARK 500 SER A 347 53.02 75.51 REMARK 500 ALA A 348 61.78 -155.32 REMARK 500 VAL A 424 -64.56 -100.19 REMARK 500 SER A 473 18.82 -140.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 220 THR A 221 145.59 REMARK 500 SER A 365 CYS A 366 -148.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 608 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4E78 RELATED DB: PDB REMARK 900 NS5B BOUND TO PRIMER-TEMPLATE WITH 3'-DG REMARK 900 RELATED ID: 4E7A RELATED DB: PDB REMARK 900 NS5B BOUND TO PRIMER-TEMPLATE WITH 2',3'-DDC REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN COMPRISES UNP RESIDUES 2443-3012 WITH RESIDUES 2886-2895 REMARK 999 REPLACED WITH A GG LINKER. DBREF 4E76 A 1 443 UNP Q99IB8 POLG_HCVJF 2443 2885 DBREF 4E76 A 454 570 UNP Q99IB8 POLG_HCVJF 2896 3012 SEQADV 4E76 MET A -1 UNP Q99IB8 EXPRESSION TAG SEQADV 4E76 SER A 0 UNP Q99IB8 EXPRESSION TAG SEQADV 4E76 GLN A 86 UNP Q99IB8 GLU 2528 ENGINEERED MUTATION SEQADV 4E76 GLN A 87 UNP Q99IB8 GLU 2529 ENGINEERED MUTATION SEQADV 4E76 GLY A 444 UNP Q99IB8 LINKER SEQADV 4E76 GLY A 445 UNP Q99IB8 LINKER SEQADV 4E76 LEU A 571 UNP Q99IB8 EXPRESSION TAG SEQADV 4E76 GLU A 572 UNP Q99IB8 EXPRESSION TAG SEQADV 4E76 HIS A 573 UNP Q99IB8 EXPRESSION TAG SEQADV 4E76 HIS A 574 UNP Q99IB8 EXPRESSION TAG SEQADV 4E76 HIS A 575 UNP Q99IB8 EXPRESSION TAG SEQADV 4E76 HIS A 576 UNP Q99IB8 EXPRESSION TAG SEQADV 4E76 HIS A 577 UNP Q99IB8 EXPRESSION TAG SEQADV 4E76 HIS A 578 UNP Q99IB8 EXPRESSION TAG SEQRES 1 A 572 MET SER SER MET SER TYR SER TRP THR GLY ALA LEU ILE SEQRES 2 A 572 THR PRO CYS SER 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 CYS 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 VAL 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 SO4 A 601 5 HET SO4 A 602 5 HET SO4 A 603 5 HET SO4 A 604 5 HET SO4 A 605 5 HET SO4 A 606 5 HET SO4 A 607 5 HET EDO A 608 4 HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 SO4 7(O4 S 2-) FORMUL 9 EDO C2 H6 O2 FORMUL 10 HOH *169(H2 O) HELIX 1 1 TYR A 33 ASN A 35 5 3 HELIX 2 2 THR A 41 LYS A 43 5 3 HELIX 3 3 SER A 44 THR A 53 1 10 HELIX 4 4 ASP A 61 LYS A 77 1 17 HELIX 5 5 THR A 84 LEU A 91 1 8 HELIX 6 6 GLY A 104 SER A 110 1 7 HELIX 7 7 SER A 112 ASP A 129 1 18 HELIX 8 8 ASP A 164 GLY A 188 1 25 HELIX 9 9 ALA A 189 TYR A 191 5 3 HELIX 10 10 SER A 196 LYS A 211 1 16 HELIX 11 11 CYS A 223 VAL A 228 1 6 HELIX 12 12 THR A 229 ALA A 242 1 14 HELIX 13 13 PRO A 246 LEU A 260 1 15 HELIX 14 14 THR A 286 GLY A 307 1 22 HELIX 15 15 GLY A 328 TYR A 346 1 19 HELIX 16 16 ASP A 359 ILE A 363 5 5 HELIX 17 17 PRO A 388 ALA A 396 1 9 HELIX 18 18 PRO A 404 TYR A 415 1 12 HELIX 19 19 THR A 418 VAL A 424 1 7 HELIX 20 20 VAL A 424 GLN A 436 1 13 HELIX 21 21 ASN A 455 LEU A 457 5 3 HELIX 22 22 ASP A 458 GLY A 468 1 11 HELIX 23 23 LEU A 469 SER A 473 5 5 HELIX 24 24 SER A 478 GLY A 493 1 16 HELIX 25 25 PRO A 496 ARG A 514 1 19 HELIX 26 26 GLY A 515 PHE A 526 1 12 HELIX 27 27 LEU A 539 LEU A 544 1 6 HELIX 28 28 LEU A 547 PHE A 551 5 5 SHEET 1 A 2 SER A 1 MET A 2 0 SHEET 2 A 2 ASP A 55 ARG A 56 -1 O ARG A 56 N SER A 1 SHEET 1 B 5 TYR A 4 TRP A 6 0 SHEET 2 B 5 THR A 273 ARG A 277 -1 O TYR A 276 N SER A 5 SHEET 3 B 5 GLY A 264 PHE A 267 -1 N MET A 266 O CYS A 274 SHEET 4 B 5 THR A 136 ALA A 140 1 N THR A 136 O PHE A 267 SHEET 5 B 5 LEU A 159 TYR A 162 -1 O ILE A 160 N MET A 139 SHEET 1 C 2 VAL A 37 CYS A 39 0 SHEET 2 C 2 VAL A 144 CYS A 146 -1 O PHE A 145 N TYR A 38 SHEET 1 D 3 PRO A 214 TYR A 219 0 SHEET 2 D 3 LEU A 320 GLU A 325 -1 O SER A 324 N MET A 215 SHEET 3 D 3 VAL A 309 VAL A 315 -1 N VAL A 309 O GLU A 325 SHEET 1 E 2 ASN A 369 LEU A 374 0 SHEET 2 E 2 ARG A 380 THR A 385 -1 O THR A 385 N ASN A 369 SITE 1 AC1 3 ARG A 48 LYS A 155 ARG A 222 SITE 1 AC2 6 PRO A 93 SER A 96 ARG A 168 LYS A 172 SITE 2 AC2 6 HOH A 797 HOH A 863 SITE 1 AC3 6 GLY A 375 PRO A 376 ARG A 377 GLY A 378 SITE 2 AC3 6 ARG A 379 ARG A 381 SITE 1 AC4 8 ARG A 422 SER A 473 MET A 474 HIS A 475 SITE 2 AC4 8 ASN A 527 TRP A 528 LYS A 533 HOH A 849 SITE 1 AC5 5 ARG A 505 VAL A 530 LYS A 531 THR A 532 SITE 2 AC5 5 HOH A 861 SITE 1 AC6 2 SER A 510 ARG A 514 SITE 1 AC7 6 PRO A 94 GLY A 104 ALA A 105 LYS A 106 SITE 2 AC7 6 GLU A 107 HOH A 771 SITE 1 AC8 3 PHE A 145 ARG A 386 THR A 390 CRYST1 140.690 140.690 92.630 90.00 90.00 120.00 P 65 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 0.007108 0.004104 0.000000 0.00000 SCALE2 0.000000 0.008207 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010796 0.00000