HEADER TRANSFERASE 24-FEB-04 1SH2 TITLE CRYSTAL STRUCTURE OF NORWALK VIRUS POLYMERASE (METAL-FREE, CENTERED TITLE 2 ORTHORHOMBIC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINUS; COMPND 5 EC: 2.7.7.48; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NORWALK VIRUS; SOURCE 3 ORGANISM_TAXID: 11983; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: XL-1 BLUE; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS RNA POLYMERASE, VIRAL ENZYME, VIRAL REPLICATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.K.NG,N.PENDAS-FRANCO,J.ROJO,J.A.BOGA,A.MACHIN,J.M.ALONSO,F.PARRA REVDAT 5 23-AUG-23 1SH2 1 REMARK REVDAT 4 13-JUL-11 1SH2 1 VERSN REVDAT 3 24-FEB-09 1SH2 1 VERSN REVDAT 2 11-JAN-05 1SH2 1 JRNL REVDAT 1 09-MAR-04 1SH2 0 JRNL AUTH K.K.NG,N.PENDAS-FRANCO,J.ROJO,J.A.BOGA,A.MACHIN,J.M.ALONSO, JRNL AUTH 2 F.PARRA JRNL TITL CRYSTAL STRUCTURE OF NORWALK VIRUS POLYMERASE REVEALS THE JRNL TITL 2 CARBOXYL TERMINUS IN THE ACTIVE SITE CLEFT. JRNL REF J.BIOL.CHEM. V. 279 16638 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 14764591 JRNL DOI 10.1074/JBC.M400584200 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 25374 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) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1596 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1691 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.3470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3939 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 40.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15000 REMARK 3 B22 (A**2) : -5.55000 REMARK 3 B33 (A**2) : 5.70000 REMARK 3 B12 (A**2) : 0.00000 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): 0.357 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.274 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.234 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.887 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.890 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4041 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5483 ; 1.070 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 501 ; 5.509 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 594 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3063 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1835 ; 0.194 ; 0.200 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): 192 ; 0.134 ; 0.200 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): 25 ; 0.138 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.192 ; 0.200 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): 2511 ; 0.991 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4065 ; 1.844 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1530 ; 2.390 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1418 ; 3.238 ; 5.000 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 209 REMARK 3 RESIDUE RANGE : A 244 A 304 REMARK 3 ORIGIN FOR THE GROUP (A): 25.0061 95.9861 43.9050 REMARK 3 T TENSOR REMARK 3 T11: 0.2175 T22: 0.2575 REMARK 3 T33: 0.0151 T12: -0.0096 REMARK 3 T13: -0.0416 T23: -0.0221 REMARK 3 L TENSOR REMARK 3 L11: 2.2296 L22: 3.8015 REMARK 3 L33: 0.5363 L12: 0.0347 REMARK 3 L13: -0.3651 L23: -0.0592 REMARK 3 S TENSOR REMARK 3 S11: 0.0107 S12: 0.1684 S13: -0.2669 REMARK 3 S21: -0.2143 S22: -0.0233 S23: 0.3148 REMARK 3 S31: -0.0507 S32: 0.0235 S33: 0.0126 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 210 A 243 REMARK 3 RESIDUE RANGE : A 305 A 389 REMARK 3 ORIGIN FOR THE GROUP (A): 35.6940 74.0730 43.9947 REMARK 3 T TENSOR REMARK 3 T11: 0.2068 T22: 0.2153 REMARK 3 T33: 0.2853 T12: -0.0389 REMARK 3 T13: 0.0259 T23: -0.0280 REMARK 3 L TENSOR REMARK 3 L11: 4.2108 L22: 5.5107 REMARK 3 L33: 2.2852 L12: -1.5010 REMARK 3 L13: 1.1376 L23: -0.0492 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: 0.2057 S13: -0.7324 REMARK 3 S21: -0.2515 S22: -0.0156 S23: -0.2782 REMARK 3 S31: 0.0938 S32: 0.2912 S33: 0.0211 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 390 A 507 REMARK 3 ORIGIN FOR THE GROUP (A): 54.5346 94.8731 51.1468 REMARK 3 T TENSOR REMARK 3 T11: 0.2414 T22: 0.3725 REMARK 3 T33: 0.4189 T12: 0.0108 REMARK 3 T13: -0.0278 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 3.1289 L22: 5.2192 REMARK 3 L33: 2.7242 L12: -2.0613 REMARK 3 L13: 1.6412 L23: -1.9903 REMARK 3 S TENSOR REMARK 3 S11: -0.2131 S12: -0.3044 S13: 0.2206 REMARK 3 S21: 0.6348 S22: 0.0479 S23: -0.3378 REMARK 3 S31: -0.3703 S32: -0.1568 S33: 0.1652 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TLS REFINEMENT WAS PERFORMED FOR EACH REMARK 3 OF THREE DOMAINS REMARK 4 REMARK 4 1SH2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021701. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27003 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 19.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.40200 REMARK 200 R SYM FOR SHELL (I) : 0.40200 REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BEAST REMARK 200 STARTING MODEL: PDB ENTRY 1KHV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM SULFATE, TRIS-CL, REMARK 280 GLYCEROL, CHAPS, 2-MERCAPTOETHANOL, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.95000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.95000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 57.13500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.62000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 57.13500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.62000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 45.95000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 57.13500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.62000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 45.95000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 57.13500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.62000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 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 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 A 630 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 649 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 GLY A 1 REMARK 465 GLY A 2 REMARK 465 ASP A 3 REMARK 465 SER A 4 REMARK 465 LYS A 5 REMARK 465 GLY A 508 REMARK 465 VAL A 509 REMARK 465 GLU A 510 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 LEU A 379 CA - CB - CG ANGL. DEV. = 14.1 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 9 67.57 23.35 REMARK 500 SER A 18 16.50 -145.86 REMARK 500 SER A 105 172.28 -57.15 REMARK 500 PRO A 303 -60.36 -29.28 REMARK 500 ASP A 373 -63.74 -105.23 REMARK 500 THR A 375 140.74 56.96 REMARK 500 GLU A 376 116.96 72.98 REMARK 500 ARG A 486 -63.20 -100.39 REMARK 500 LEU A 490 25.89 -143.80 REMARK 500 ASN A 505 -146.63 -71.04 REMARK 500 GLU A 506 59.80 25.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KHV RELATED DB: PDB REMARK 900 RHDV RNA POLYMERASE REMARK 900 RELATED ID: 1SH0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NORWALK VIRUS POLYMERASE (TRICLINIC) REMARK 900 RELATED ID: 1SH3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NORWALK VIRUS POLYMERASE (MGSO4 CRYSTAL FORM) DBREF 1SH2 A 1 510 UNP Q70ET3 Q70ET3_9CALI 329 838 SEQRES 1 A 510 GLY GLY ASP SER LYS GLY THR TYR CYS GLY ALA PRO ILE SEQRES 2 A 510 LEU GLY PRO GLY SER ALA PRO LYS LEU SER THR LYS THR SEQRES 3 A 510 LYS PHE TRP ARG SER SER THR ALA PRO LEU PRO PRO GLY SEQRES 4 A 510 THR TYR GLU PRO ALA TYR LEU GLY GLY LYS ASP PRO ARG SEQRES 5 A 510 VAL LYS GLY GLY PRO SER LEU GLN GLN VAL MET ARG ASP SEQRES 6 A 510 GLN LEU LYS PRO PHE THR GLU PRO ARG GLY LYS PRO PRO SEQRES 7 A 510 LYS PRO SER VAL LEU GLU ALA ALA LYS LYS THR ILE ILE SEQRES 8 A 510 ASN VAL LEU GLU GLN THR ILE ASP PRO PRO ASP LYS TRP SEQRES 9 A 510 SER PHE ALA GLN ALA CYS ALA SER LEU ASP LYS THR THR SEQRES 10 A 510 SER SER GLY HIS PRO HIS HIS MET ARG LYS ASN ASP CYS SEQRES 11 A 510 TRP ASN GLY GLU SER PHE THR GLY LYS LEU ALA ASP GLN SEQRES 12 A 510 ALA SER LYS ALA ASN LEU MET PHE GLU GLU GLY LYS ASN SEQRES 13 A 510 MET THR PRO VAL TYR THR GLY ALA LEU LYS ASP GLU LEU SEQRES 14 A 510 VAL LYS THR ASP LYS ILE TYR GLY LYS ILE LYS LYS ARG SEQRES 15 A 510 LEU LEU TRP GLY SER ASP LEU ALA THR MET ILE ARG CYS SEQRES 16 A 510 ALA ARG ALA PHE GLY GLY LEU MET ASP GLU LEU LYS THR SEQRES 17 A 510 HIS CYS VAL THR LEU PRO ILE ARG VAL GLY MET ASN MET SEQRES 18 A 510 ASN GLU ASP GLY PRO ILE ILE PHE GLU ARG HIS SER ARG SEQRES 19 A 510 TYR ARG TYR HIS TYR ASP ALA ASP TYR SER ARG TRP ASP SEQRES 20 A 510 SER THR GLN GLN ARG ALA VAL LEU ALA ALA ALA LEU GLU SEQRES 21 A 510 ILE MET VAL LYS PHE SER SER GLU PRO HIS LEU ALA GLN SEQRES 22 A 510 VAL VAL ALA GLU ASP LEU LEU SER PRO SER VAL VAL ASP SEQRES 23 A 510 VAL GLY ASP PHE THR ILE SER ILE ASN GLU GLY LEU PRO SEQRES 24 A 510 SER GLY VAL PRO CYS THR SER GLN TRP ASN SER ILE ALA SEQRES 25 A 510 HIS TRP LEU LEU THR LEU CYS ALA LEU SER GLU VAL THR SEQRES 26 A 510 ASN LEU SER PRO ASP ILE ILE GLN ALA ASN SER LEU PHE SEQRES 27 A 510 SER PHE TYR GLY ASP ASP GLU ILE VAL SER THR ASP ILE SEQRES 28 A 510 LYS LEU ASP PRO GLU LYS LEU THR ALA LYS LEU LYS GLU SEQRES 29 A 510 TYR GLY LEU LYS PRO THR ARG PRO ASP LYS THR GLU GLY SEQRES 30 A 510 PRO LEU VAL ILE SER GLU ASP LEU ASN GLY LEU THR PHE SEQRES 31 A 510 LEU ARG ARG THR VAL THR ARG ASP PRO ALA GLY TRP PHE SEQRES 32 A 510 GLY LYS LEU GLU GLN SER SER ILE LEU ARG GLN MET TYR SEQRES 33 A 510 TRP THR ARG GLY PRO ASN HIS GLU ASP PRO SER GLU THR SEQRES 34 A 510 MET ILE PRO HIS SER GLN ARG PRO ILE GLN LEU MET SER SEQRES 35 A 510 LEU LEU GLY GLU ALA ALA LEU HIS GLY PRO ALA PHE TYR SEQRES 36 A 510 SER LYS ILE SER LYS LEU VAL ILE ALA GLU LEU LYS GLU SEQRES 37 A 510 GLY GLY MET ASP PHE TYR VAL PRO ARG GLN GLU PRO MET SEQRES 38 A 510 PHE ARG TRP MET ARG PHE SER ASP LEU SER THR TRP GLU SEQRES 39 A 510 GLY ASP ARG ASN LEU ALA PRO SER PHE VAL ASN GLU ASP SEQRES 40 A 510 GLY VAL GLU FORMUL 2 HOH *139(H2 O) HELIX 1 1 SER A 58 GLU A 72 1 15 HELIX 2 2 LYS A 79 GLN A 96 1 18 HELIX 3 3 SER A 105 LEU A 113 1 9 HELIX 4 4 ARG A 126 TRP A 131 5 6 HELIX 5 5 GLY A 138 GLU A 153 1 16 HELIX 6 6 THR A 172 GLY A 177 1 6 HELIX 7 7 ASP A 188 HIS A 209 1 22 HELIX 8 8 ASN A 220 ARG A 234 1 15 HELIX 9 9 ARG A 245 GLN A 250 1 6 HELIX 10 10 GLN A 251 SER A 266 1 16 HELIX 11 11 GLU A 268 SER A 281 1 14 HELIX 12 12 CYS A 304 ASN A 326 1 23 HELIX 13 13 SER A 328 ASN A 335 1 8 HELIX 14 14 ASP A 354 TYR A 365 1 12 HELIX 15 15 GLU A 407 TYR A 416 1 10 HELIX 16 16 GLN A 435 ALA A 448 1 14 HELIX 17 17 GLY A 451 GLY A 469 1 19 HELIX 18 18 ARG A 477 SER A 488 1 12 HELIX 19 19 ASP A 496 ALA A 500 5 5 SHEET 1 A 6 THR A 7 TYR A 8 0 SHEET 2 A 6 ALA A 11 PRO A 16 -1 O ALA A 11 N TYR A 8 SHEET 3 A 6 PHE A 290 ILE A 294 -1 O THR A 291 N LEU A 14 SHEET 4 A 6 SER A 283 ASP A 286 -1 N VAL A 285 O ILE A 292 SHEET 5 A 6 VAL A 160 LEU A 165 1 N TYR A 161 O ASP A 286 SHEET 6 A 6 LEU A 183 GLY A 186 -1 O LEU A 184 N ALA A 164 SHEET 1 B 2 THR A 26 ARG A 30 0 SHEET 2 B 2 TRP A 417 HIS A 423 -1 O GLY A 420 N LYS A 27 SHEET 1 C 2 GLU A 42 PRO A 43 0 SHEET 2 C 2 LEU A 169 VAL A 170 -1 O VAL A 170 N GLU A 42 SHEET 1 D 3 TYR A 237 TYR A 239 0 SHEET 2 D 3 ASP A 344 THR A 349 -1 O THR A 349 N TYR A 237 SHEET 3 D 3 SER A 336 TYR A 341 -1 N LEU A 337 O SER A 348 SHEET 1 E 2 ASP A 242 TYR A 243 0 SHEET 2 E 2 PRO A 369 THR A 370 -1 O THR A 370 N ASP A 242 SHEET 1 F 3 THR A 389 PHE A 390 0 SHEET 2 F 3 ARG A 393 ASP A 398 -1 O ARG A 393 N PHE A 390 SHEET 3 F 3 GLY A 401 LEU A 406 -1 O PHE A 403 N THR A 396 CISPEP 1 HIS A 121 PRO A 122 0 -6.48 CRYST1 114.270 115.240 91.900 90.00 90.00 90.00 C 2 2 21 8 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 0.008751 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008678 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010881 0.00000 TER 3940 ASP A 507 HETATM 3941 O HOH A 511 28.826 67.319 30.995 1.00 48.13 O HETATM 3942 O HOH A 512 30.663 58.564 38.444 1.00 56.69 O HETATM 3943 O HOH A 513 35.737 57.829 43.015 1.00 44.84 O HETATM 3944 O HOH A 514 33.728 57.177 50.775 1.00 70.65 O HETATM 3945 O HOH A 515 30.640 58.569 51.424 1.00 46.79 O HETATM 3946 O HOH A 516 39.724 63.005 53.243 1.00 53.47 O HETATM 3947 O HOH A 517 32.676 69.663 53.036 1.00 44.30 O HETATM 3948 O HOH A 518 30.990 70.121 55.201 1.00 52.27 O HETATM 3949 O HOH A 519 32.980 72.415 51.813 1.00 44.17 O HETATM 3950 O HOH A 520 26.693 68.382 57.492 1.00 45.61 O HETATM 3951 O HOH A 521 32.602 76.711 62.533 1.00 51.20 O HETATM 3952 O HOH A 522 37.536 81.431 62.799 1.00 43.41 O HETATM 3953 O HOH A 523 35.970 84.325 61.741 1.00 57.81 O HETATM 3954 O HOH A 524 38.459 85.300 61.339 1.00 58.81 O HETATM 3955 O HOH A 525 43.963 91.760 61.698 1.00 49.48 O HETATM 3956 O HOH A 526 50.873 88.860 60.115 1.00 56.31 O HETATM 3957 O HOH A 527 48.260 82.050 54.409 1.00 42.46 O HETATM 3958 O HOH A 528 48.988 86.822 51.022 1.00 37.72 O HETATM 3959 O HOH A 529 47.575 92.417 51.375 1.00 49.16 O HETATM 3960 O HOH A 530 52.208 98.039 57.784 1.00 52.68 O HETATM 3961 O HOH A 531 46.492 103.008 47.955 1.00 42.95 O HETATM 3962 O HOH A 532 47.610 100.989 45.492 1.00 49.74 O HETATM 3963 O HOH A 533 42.252 98.111 41.550 1.00 49.99 O HETATM 3964 O HOH A 534 39.743 98.800 43.255 1.00 53.54 O HETATM 3965 O HOH A 535 37.185 100.477 45.850 1.00 54.66 O HETATM 3966 O HOH A 536 34.656 102.453 41.589 1.00 41.96 O HETATM 3967 O HOH A 537 33.938 105.336 38.304 1.00 37.26 O HETATM 3968 O HOH A 538 34.980 107.288 39.721 1.00 44.58 O HETATM 3969 O HOH A 539 37.121 106.989 42.097 1.00 42.80 O HETATM 3970 O HOH A 540 36.617 105.590 36.878 1.00 43.46 O HETATM 3971 O HOH A 541 39.202 104.290 36.375 1.00 39.49 O HETATM 3972 O HOH A 542 36.511 98.432 35.415 1.00 38.05 O HETATM 3973 O HOH A 543 36.648 94.564 32.893 1.00 50.79 O HETATM 3974 O HOH A 544 41.893 93.568 33.774 1.00 51.31 O HETATM 3975 O HOH A 545 46.235 89.640 38.019 1.00 46.40 O HETATM 3976 O HOH A 546 47.220 89.157 40.734 1.00 37.78 O HETATM 3977 O HOH A 547 53.323 85.285 41.371 1.00 47.13 O HETATM 3978 O HOH A 548 52.307 83.700 43.309 1.00 59.28 O HETATM 3979 O HOH A 549 40.398 80.333 42.263 1.00 32.65 O HETATM 3980 O HOH A 550 39.140 86.854 44.316 1.00 40.59 O HETATM 3981 O HOH A 551 36.741 91.694 40.969 1.00 57.23 O HETATM 3982 O HOH A 552 34.676 88.965 39.492 1.00 51.80 O HETATM 3983 O HOH A 553 33.911 86.695 37.156 1.00 47.83 O HETATM 3984 O HOH A 554 31.327 89.198 37.951 1.00 34.64 O HETATM 3985 O HOH A 555 29.408 90.025 35.519 1.00 44.07 O HETATM 3986 O HOH A 556 35.240 89.176 34.103 1.00 38.91 O HETATM 3987 O HOH A 557 38.103 90.650 28.280 1.00 43.05 O HETATM 3988 O HOH A 558 32.929 97.598 26.025 1.00 55.12 O HETATM 3989 O HOH A 559 32.423 98.022 28.570 1.00 34.22 O HETATM 3990 O HOH A 560 34.166 100.043 23.826 1.00 49.79 O HETATM 3991 O HOH A 561 36.618 100.230 22.726 1.00 46.85 O HETATM 3992 O HOH A 562 39.013 100.546 30.832 1.00 37.60 O HETATM 3993 O HOH A 563 33.031 106.072 34.689 1.00 38.41 O HETATM 3994 O HOH A 564 31.166 105.637 36.897 1.00 33.67 O HETATM 3995 O HOH A 565 29.697 107.322 38.359 1.00 50.52 O HETATM 3996 O HOH A 566 25.552 107.721 38.423 1.00 48.69 O HETATM 3997 O HOH A 567 26.318 108.382 41.450 1.00 42.40 O HETATM 3998 O HOH A 568 24.416 107.890 43.163 1.00 30.47 O HETATM 3999 O HOH A 569 26.266 104.042 41.585 1.00 40.78 O HETATM 4000 O HOH A 570 24.324 103.618 45.593 1.00 40.28 O HETATM 4001 O HOH A 571 25.455 99.678 46.244 1.00 42.59 O HETATM 4002 O HOH A 572 27.639 101.448 49.913 1.00 46.26 O HETATM 4003 O HOH A 573 26.896 100.316 52.617 1.00 40.83 O HETATM 4004 O HOH A 574 31.097 100.039 50.012 1.00 45.71 O HETATM 4005 O HOH A 575 27.637 94.751 47.818 1.00 60.48 O HETATM 4006 O HOH A 576 29.722 92.110 49.081 1.00 39.53 O HETATM 4007 O HOH A 577 33.784 91.113 50.771 1.00 43.82 O HETATM 4008 O HOH A 578 31.051 88.500 44.507 1.00 46.02 O HETATM 4009 O HOH A 579 32.865 87.811 42.834 1.00 36.39 O HETATM 4010 O HOH A 580 30.269 91.008 42.160 1.00 35.62 O HETATM 4011 O HOH A 581 33.191 94.302 40.961 1.00 50.93 O HETATM 4012 O HOH A 582 29.009 105.630 45.668 1.00 36.93 O HETATM 4013 O HOH A 583 20.496 103.784 43.521 1.00 36.59 O HETATM 4014 O HOH A 584 18.862 99.151 45.240 1.00 50.39 O HETATM 4015 O HOH A 585 13.783 101.231 47.547 1.00 41.01 O HETATM 4016 O HOH A 586 12.921 105.268 49.168 1.00 53.26 O HETATM 4017 O HOH A 587 12.972 110.027 50.275 1.00 42.16 O HETATM 4018 O HOH A 588 19.097 108.444 48.075 1.00 35.06 O HETATM 4019 O HOH A 589 16.511 111.330 41.100 1.00 54.16 O HETATM 4020 O HOH A 590 17.688 108.066 39.888 1.00 47.16 O HETATM 4021 O HOH A 591 19.267 114.147 39.683 1.00 42.77 O HETATM 4022 O HOH A 592 23.487 111.388 33.764 1.00 42.11 O HETATM 4023 O HOH A 593 27.484 109.924 31.431 1.00 33.05 O HETATM 4024 O HOH A 594 28.460 109.329 28.230 1.00 58.58 O HETATM 4025 O HOH A 595 32.246 110.214 27.746 1.00 45.16 O HETATM 4026 O HOH A 596 30.380 106.924 21.585 1.00 60.04 O HETATM 4027 O HOH A 597 28.366 86.893 29.940 1.00 60.11 O HETATM 4028 O HOH A 598 30.370 82.660 34.153 1.00 40.46 O HETATM 4029 O HOH A 599 24.207 80.408 35.613 1.00 40.27 O HETATM 4030 O HOH A 600 23.411 80.932 38.175 1.00 41.41 O HETATM 4031 O HOH A 601 23.316 82.114 32.276 1.00 44.45 O HETATM 4032 O HOH A 602 16.853 79.421 30.876 1.00 50.56 O HETATM 4033 O HOH A 603 14.848 83.512 32.748 1.00 44.48 O HETATM 4034 O HOH A 604 16.454 82.019 36.122 1.00 48.47 O HETATM 4035 O HOH A 605 15.914 75.092 37.676 1.00 52.99 O HETATM 4036 O HOH A 606 15.229 74.805 44.788 1.00 48.07 O HETATM 4037 O HOH A 607 14.342 77.384 45.027 1.00 45.15 O HETATM 4038 O HOH A 608 14.035 77.303 52.501 1.00 56.99 O HETATM 4039 O HOH A 609 13.100 80.111 53.289 1.00 53.53 O HETATM 4040 O HOH A 610 12.552 83.786 50.342 1.00 30.72 O HETATM 4041 O HOH A 611 12.167 84.630 48.179 1.00 36.82 O HETATM 4042 O HOH A 612 4.840 86.801 48.919 1.00 50.67 O HETATM 4043 O HOH A 613 5.318 89.156 51.187 1.00 60.59 O HETATM 4044 O HOH A 614 10.695 94.880 43.857 1.00 47.66 O HETATM 4045 O HOH A 615 11.290 94.799 40.788 1.00 53.60 O HETATM 4046 O HOH A 616 8.567 94.774 39.154 1.00 57.27 O HETATM 4047 O HOH A 617 7.283 100.325 41.155 1.00 48.69 O HETATM 4048 O HOH A 618 14.474 96.625 41.308 1.00 40.65 O HETATM 4049 O HOH A 619 14.724 93.884 41.899 1.00 29.22 O HETATM 4050 O HOH A 620 23.282 96.772 53.493 1.00 43.27 O HETATM 4051 O HOH A 621 20.182 90.316 61.788 1.00 44.43 O HETATM 4052 O HOH A 622 15.908 89.195 59.491 1.00 34.37 O HETATM 4053 O HOH A 623 24.976 87.588 64.569 1.00 53.62 O HETATM 4054 O HOH A 624 25.605 90.519 64.485 1.00 43.78 O HETATM 4055 O HOH A 625 23.882 92.437 67.513 1.00 46.48 O HETATM 4056 O HOH A 626 25.786 95.685 64.530 1.00 57.80 O HETATM 4057 O HOH A 627 24.102 104.333 64.120 1.00 49.62 O HETATM 4058 O HOH A 628 29.129 104.868 60.219 1.00 43.38 O HETATM 4059 O HOH A 629 31.876 104.599 56.613 1.00 36.48 O HETATM 4060 O HOH A 630 25.080 115.249 45.958 0.50 36.71 O HETATM 4061 O HOH A 631 17.402 115.942 60.084 1.00 52.83 O HETATM 4062 O HOH A 632 13.235 100.638 64.876 1.00 46.91 O HETATM 4063 O HOH A 633 18.822 100.725 68.682 1.00 51.53 O HETATM 4064 O HOH A 634 28.933 86.866 55.658 1.00 47.65 O HETATM 4065 O HOH A 635 30.977 81.991 55.941 1.00 46.11 O HETATM 4066 O HOH A 636 39.866 72.956 60.084 1.00 44.82 O HETATM 4067 O HOH A 637 50.696 71.689 57.905 1.00 53.84 O HETATM 4068 O HOH A 638 53.406 69.873 48.791 1.00 54.52 O HETATM 4069 O HOH A 639 41.765 74.489 36.625 1.00 57.73 O HETATM 4070 O HOH A 640 33.093 74.756 40.682 1.00 40.80 O HETATM 4071 O HOH A 641 13.364 72.664 57.682 1.00 55.69 O HETATM 4072 O HOH A 642 49.987 94.795 36.649 1.00 42.57 O HETATM 4073 O HOH A 643 57.007 101.803 44.663 1.00 47.03 O HETATM 4074 O HOH A 644 59.827 103.331 42.438 1.00 52.18 O HETATM 4075 O HOH A 645 62.819 97.297 40.904 1.00 51.01 O HETATM 4076 O HOH A 646 66.896 97.573 58.543 1.00 51.70 O HETATM 4077 O HOH A 647 65.930 93.899 59.377 1.00 52.91 O HETATM 4078 O HOH A 648 58.470 86.825 68.760 1.00 85.49 O HETATM 4079 O HOH A 649 51.698 115.234 45.952 0.50 60.50 O MASTER 387 0 0 19 18 0 0 6 4078 1 0 40 END