HEADER VIRAL PROTEIN 24-FEB-17 5N8X TITLE TRIGONAL STRUCTURE OF MUTANT V173I OF 3D POLYMERASE FROM FOOT-AND- TITLE 2 MOUTH DISEASE VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3D POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FOOT-AND-MOUTH DISEASE VIRUS; SOURCE 3 ORGANISM_TAXID: 12110; SOURCE 4 GENE: CDS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS 3DPOLYMERASE, RNA DEPENDENT RNA POLYMERASES, 5'-FLUORACIL, NUCLEOTIDE KEYWDS 2 ANALOGUES, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.FERRER-ORTA,N.VERDAGUER REVDAT 3 17-JAN-24 5N8X 1 REMARK REVDAT 2 31-MAY-17 5N8X 1 JRNL REVDAT 1 10-MAY-17 5N8X 0 JRNL AUTH I.DE LA HIGUERA,C.FERRER-ORTA,A.I.DE AVILA,C.PERALES, JRNL AUTH 2 M.SIERRA,K.SINGH,S.G.SARAFIANOS,Y.DEHOUCK,U.BASTOLLA, JRNL AUTH 3 N.VERDAGUER,E.DOMINGO JRNL TITL MOLECULAR AND FUNCTIONAL BASES OF SELECTION AGAINST A JRNL TITL 2 MUTATION BIAS IN AN RNA VIRUS. JRNL REF GENOME BIOL EVOL V. 9 1212 2017 JRNL REFN ISSN 1759-6653 JRNL PMID 28460010 JRNL DOI 10.1093/GBE/EVX075 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 18995 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) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.252 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 991 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1311 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3743 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 32 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.26000 REMARK 3 B12 (A**2) : 0.04000 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): 0.604 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.307 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.287 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.761 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3821 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3509 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5167 ; 1.159 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8119 ; 0.969 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 469 ; 6.124 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 181 ;37.367 ;23.481 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 625 ;16.017 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;16.996 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 564 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4264 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 815 ; 0.002 ; 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): 1882 ; 0.124 ; 3.259 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1881 ; 0.124 ; 3.258 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2349 ; 0.237 ; 4.886 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2350 ; 0.237 ; 4.887 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1938 ; 0.045 ; 3.298 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1938 ; 0.046 ; 3.298 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2819 ; 0.104 ; 4.923 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 15560 ; 1.564 ;61.246 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 15560 ; 1.564 ;61.244 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 : 1 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 1 A 475 REMARK 3 ORIGIN FOR THE GROUP (A): 18.2996 26.6133 23.7697 REMARK 3 T TENSOR REMARK 3 T11: 0.1279 T22: 0.2534 REMARK 3 T33: 0.2908 T12: -0.0451 REMARK 3 T13: -0.0203 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 1.2458 L22: 5.9471 REMARK 3 L33: 2.1920 L12: -0.6897 REMARK 3 L13: 1.1271 L23: -1.4837 REMARK 3 S TENSOR REMARK 3 S11: -0.1098 S12: 0.0840 S13: 0.0357 REMARK 3 S21: -0.4884 S22: 0.2662 S23: 0.4821 REMARK 3 S31: 0.1077 S32: -0.3483 S33: -0.1565 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 REMARK 4 REMARK 4 5N8X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003686. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20009 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 46.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.43100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC RIGID BODY REFINEMENT REMARK 200 STARTING MODEL: 1WNR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 36% PEG 4000, 0.2M AMMONIUM ACETATE REMARK 280 0.1M MES(2-(N-MORPHOLINO) ETHANESULFONIC ACID) PH 6.0 4% GAMMA- REMARK 280 BUTYROLACTONE., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 66.41733 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 33.20867 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 33.20867 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 66.41733 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 TOTAL BURIED SURFACE AREA: 1370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 HIS A 476 REMARK 465 HIS A 477 REMARK 465 HIS A 478 REMARK 465 HIS A 479 REMARK 465 HIS A 480 REMARK 465 HIS A 481 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 LYS A 369 CG CD CE NZ REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 VAL A 15 REMARK 475 MET A 16 REMARK 475 ARG A 17 REMARK 475 LYS A 18 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 NZ LYS A 148 OE2 GLU A 151 2.18 REMARK 500 CG LEU A 163 OH TYR A 285 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 14 C VAL A 15 N -0.174 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 CYS A 300 CA - CB - SG ANGL. DEV. = 9.3 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 17 0.05 88.60 REMARK 500 GLU A 33 43.89 -81.53 REMARK 500 ASP A 114 -10.25 81.15 REMARK 500 ARG A 153 64.47 60.93 REMARK 500 PHE A 261 46.85 -106.96 REMARK 500 ALA A 284 42.47 -89.48 REMARK 500 GLU A 286 -111.05 48.45 REMARK 500 ASN A 287 27.65 -75.68 REMARK 500 LYS A 288 -107.91 64.92 REMARK 500 ARG A 289 95.13 -67.61 REMARK 500 SER A 298 87.49 -69.93 REMARK 500 CYS A 300 -39.23 -138.87 REMARK 500 SER A 301 -18.38 125.18 REMARK 500 SER A 370 -145.54 -129.07 REMARK 500 ASP A 371 -128.15 47.48 REMARK 500 CYS A 467 134.94 -176.11 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 GLU A 154 TYR A 155 -147.46 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 MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WNE RELATED DB: PDB REMARK 900 STRUCTURE OF THE RNA DEPENDENT RNA POLYMERASE FROM FMDV WITH RNA REMARK 900 TEMPLATE -PRIMER REMARK 900 RELATED ID: 1U09 RELATED DB: PDB REMARK 900 STRUCTURE OF THE RNA DEPENDENT RNA POLYMERASE FROM FMDV DBREF 5N8X A 1 470 UNP A4H1Z0 A4H1Z0_9PICO 1858 2327 SEQADV 5N8X ILE A 173 UNP A4H1Z0 VAL 2030 ENGINEERED MUTATION SEQADV 5N8X ALA A 471 UNP A4H1Z0 EXPRESSION TAG SEQADV 5N8X ALA A 472 UNP A4H1Z0 EXPRESSION TAG SEQADV 5N8X ALA A 473 UNP A4H1Z0 EXPRESSION TAG SEQADV 5N8X LEU A 474 UNP A4H1Z0 EXPRESSION TAG SEQADV 5N8X GLU A 475 UNP A4H1Z0 EXPRESSION TAG SEQADV 5N8X HIS A 476 UNP A4H1Z0 EXPRESSION TAG SEQADV 5N8X HIS A 477 UNP A4H1Z0 EXPRESSION TAG SEQADV 5N8X HIS A 478 UNP A4H1Z0 EXPRESSION TAG SEQADV 5N8X HIS A 479 UNP A4H1Z0 EXPRESSION TAG SEQADV 5N8X HIS A 480 UNP A4H1Z0 EXPRESSION TAG SEQADV 5N8X HIS A 481 UNP A4H1Z0 EXPRESSION TAG SEQRES 1 A 481 GLY LEU ILE VAL ASP THR ARG ASP VAL GLU GLU ARG VAL SEQRES 2 A 481 HIS VAL MET ARG LYS THR LYS LEU ALA PRO THR VAL ALA SEQRES 3 A 481 HIS GLY VAL PHE ASN PRO GLU PHE GLY PRO ALA ALA LEU SEQRES 4 A 481 SER ASN LYS ASP PRO ARG LEU ASN GLU GLY VAL VAL LEU SEQRES 5 A 481 ASP GLU VAL ILE PHE SER LYS HIS LYS GLY ASP THR LYS SEQRES 6 A 481 MET SER ALA GLU ASP LYS ALA LEU PHE ARG ARG CYS ALA SEQRES 7 A 481 ALA ASP TYR ALA SER ARG LEU HIS SER VAL LEU GLY THR SEQRES 8 A 481 ALA ASN ALA PRO LEU SER ILE TYR GLU ALA ILE LYS GLY SEQRES 9 A 481 VAL ASP GLY LEU ASP ALA MET GLU PRO ASP THR ALA PRO SEQRES 10 A 481 GLY LEU PRO TRP ALA LEU GLN GLY LYS ARG ARG GLY ALA SEQRES 11 A 481 LEU ILE ASP PHE GLU ASN GLY THR VAL GLY PRO GLU VAL SEQRES 12 A 481 GLU ALA ALA LEU LYS LEU MET GLU LYS ARG GLU TYR LYS SEQRES 13 A 481 PHE ALA CYS GLN THR PHE LEU LYS ASP GLU ILE ARG PRO SEQRES 14 A 481 MET GLU LYS ILE ARG ALA GLY LYS THR ARG ILE VAL ASP SEQRES 15 A 481 VAL LEU PRO VAL GLU HIS ILE LEU TYR THR ARG MET MET SEQRES 16 A 481 ILE GLY ARG PHE CYS ALA GLN MET HIS SER ASN ASN GLY SEQRES 17 A 481 PRO GLN ILE GLY SER ALA VAL GLY CYS ASN PRO ASP VAL SEQRES 18 A 481 ASP TRP GLN ARG PHE GLY THR HIS PHE ALA GLN TYR ARG SEQRES 19 A 481 ASN VAL TRP ASP VAL ASP TYR SER ALA PHE ASP ALA ASN SEQRES 20 A 481 HIS CYS SER ASP ALA MET ASN ILE MET PHE GLU GLU VAL SEQRES 21 A 481 PHE ARG THR GLU PHE GLY PHE HIS PRO ASN ALA GLU TRP SEQRES 22 A 481 ILE LEU LYS THR LEU VAL ASN THR GLU HIS ALA TYR GLU SEQRES 23 A 481 ASN LYS ARG ILE THR VAL GLU GLY GLY MET PRO SER GLY SEQRES 24 A 481 CYS SER ALA THR SER ILE ILE ASN THR ILE LEU ASN ASN SEQRES 25 A 481 ILE TYR VAL LEU TYR ALA LEU ARG ARG HIS TYR GLU GLY SEQRES 26 A 481 VAL GLU LEU ASP THR TYR THR MET ILE SER TYR GLY ASP SEQRES 27 A 481 ASP ILE VAL VAL ALA SER ASP TYR ASP LEU ASP PHE GLU SEQRES 28 A 481 ALA LEU LYS PRO HIS PHE LYS SER LEU GLY GLN THR ILE SEQRES 29 A 481 THR PRO ALA ASP LYS SER ASP LYS GLY PHE VAL LEU GLY SEQRES 30 A 481 HIS SER ILE THR ASP VAL THR PHE LEU LYS ARG HIS PHE SEQRES 31 A 481 HIS MET ASP TYR GLY THR GLY PHE TYR LYS PRO VAL MET SEQRES 32 A 481 ALA SER LYS THR LEU GLU ALA ILE LEU SER PHE ALA ARG SEQRES 33 A 481 ARG GLY THR ILE GLN GLU LYS LEU ILE SER VAL ALA GLY SEQRES 34 A 481 LEU ALA VAL HIS SER GLY PRO ASP GLU TYR ARG ARG LEU SEQRES 35 A 481 PHE GLU PRO PHE GLN GLY LEU PHE GLU ILE PRO SER TYR SEQRES 36 A 481 ARG SER LEU TYR LEU ARG TRP VAL ASN ALA VAL CYS GLY SEQRES 37 A 481 ASP ALA ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS HET MN A 501 1 HET GOL A 502 6 HET GOL A 503 6 HET GOL A 504 6 HET GOL A 505 6 HET GOL A 506 6 HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MN MN 2+ FORMUL 3 GOL 5(C3 H8 O3) FORMUL 8 HOH *32(H2 O) HELIX 1 AA1 THR A 24 ASN A 31 1 8 HELIX 2 AA2 VAL A 51 ILE A 56 1 6 HELIX 3 AA3 SER A 67 GLY A 90 1 24 HELIX 4 AA4 SER A 97 GLY A 104 1 8 HELIX 5 AA5 ARG A 127 LEU A 131 1 5 HELIX 6 AA6 GLY A 140 LYS A 152 1 13 HELIX 7 AA7 MET A 170 ALA A 175 1 6 HELIX 8 AA8 PRO A 185 ASN A 206 1 22 HELIX 9 AA9 ASN A 207 GLY A 212 5 6 HELIX 10 AB1 ASN A 218 GLN A 232 1 15 HELIX 11 AB2 CYS A 249 PHE A 261 1 13 HELIX 12 AB3 ARG A 262 GLY A 266 5 5 HELIX 13 AB4 PRO A 269 THR A 277 1 9 HELIX 14 AB5 ALA A 302 TYR A 323 1 22 HELIX 15 AB6 GLU A 327 TYR A 331 5 5 HELIX 16 AB7 ASP A 349 SER A 359 1 11 HELIX 17 AB8 SER A 379 ASP A 382 5 4 HELIX 18 AB9 ALA A 404 SER A 413 1 10 HELIX 19 AC1 THR A 419 VAL A 432 1 14 HELIX 20 AC2 GLY A 435 PHE A 443 1 9 HELIX 21 AC3 GLU A 444 GLN A 447 5 4 HELIX 22 AC4 SER A 454 CYS A 467 1 14 HELIX 23 AC5 CYS A 467 ALA A 473 1 7 SHEET 1 AA1 3 LEU A 2 THR A 6 0 SHEET 2 AA1 3 LYS A 288 GLU A 293 -1 O GLU A 293 N LEU A 2 SHEET 3 AA1 3 ASN A 280 TYR A 285 -1 N HIS A 283 O ILE A 290 SHEET 1 AA2 2 LEU A 21 PRO A 23 0 SHEET 2 AA2 2 PHE A 414 ARG A 416 -1 O ALA A 415 N ALA A 22 SHEET 1 AA3 2 PHE A 34 PRO A 36 0 SHEET 2 AA3 2 ILE A 167 PRO A 169 -1 O ARG A 168 N GLY A 35 SHEET 1 AA4 2 ILE A 132 ASP A 133 0 SHEET 2 AA4 2 THR A 138 VAL A 139 -1 O THR A 138 N ASP A 133 SHEET 1 AA5 2 GLN A 160 LEU A 163 0 SHEET 2 AA5 2 ILE A 180 VAL A 183 -1 O VAL A 183 N GLN A 160 SHEET 1 AA6 4 THR A 332 TYR A 336 0 SHEET 2 AA6 4 ASP A 339 SER A 344 -1 O ASP A 339 N TYR A 336 SHEET 3 AA6 4 ASN A 235 TYR A 241 -1 N TRP A 237 O VAL A 342 SHEET 4 AA6 4 ILE A 364 PRO A 366 -1 O THR A 365 N ASP A 240 SHEET 1 AA7 3 THR A 384 PHE A 385 0 SHEET 2 AA7 3 ARG A 388 MET A 392 -1 O ARG A 388 N PHE A 385 SHEET 3 AA7 3 TYR A 399 VAL A 402 -1 O VAL A 402 N HIS A 389 LINK OD1 ASP A 238 MN MN A 501 1555 1555 2.51 CISPEP 1 LEU A 119 PRO A 120 0 -1.97 SITE 1 AC1 4 ASP A 238 ASP A 240 ASP A 339 THR A 384 SITE 1 AC2 3 ILE A 167 THR A 407 ILE A 411 SITE 1 AC3 3 ARG A 262 GLU A 272 HOH A 619 SITE 1 AC4 6 TYR A 81 ARG A 84 PRO A 209 GLN A 210 SITE 2 AC4 6 ASN A 312 LEU A 328 SITE 1 AC5 8 VAL A 236 TRP A 237 ASP A 238 PRO A 366 SITE 2 AC5 8 ALA A 367 ASP A 368 VAL A 375 HIS A 378 SITE 1 AC6 3 ARG A 262 GLU A 264 TYR A 455 CRYST1 93.506 93.506 99.626 90.00 90.00 120.00 P 32 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 0.010695 0.006174 0.000000 0.00000 SCALE2 0.000000 0.012349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010038 0.00000