HEADER TRANSFERASE/RNA 26-JAN-07 2E9R TITLE FOOT-AND-MOUTH DISEASE VIRUS RNA-DEPENDENT RNA POLYMERASE IN COMPLEX TITLE 2 WITH A TEMPLATE-PRIMER RNA AND WITH RIBAVIRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*CP*AP*UP*GP*GP*GP*CP*CP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: RNA TEMPLATE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*CP*CP*C*GP*GP*GP*CP*CP*C)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: RNA PRIMER; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA-DEPENDENT RNA POLYMERASE; COMPND 13 CHAIN: X; COMPND 14 EC: 2.7.7.48; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY A COMMERCIAL.; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY A COMMERCIAL.; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: FOOT-AND-MOUTH DISEASE VIRUS C-S8C1; SOURCE 9 ORGANISM_TAXID: 244367; SOURCE 10 STRAIN: C-S8C1; SOURCE 11 GENE: 3D; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS FOOT-AND-MOUTH DISEASE VIRUS, RNA-DEPENDENT RNA POLYMERASE, 3D KEYWDS 2 POLYMERASE, POLYMERASE, TRANSFERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.FERRER-ORTA,A.ARIAS,R.PEREZ-LUQUE,C.ESCARMIS,E.DOMINGO,N.VERDAGUER REVDAT 3 25-OCT-23 2E9R 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2E9R 1 VERSN REVDAT 1 26-JUN-07 2E9R 0 JRNL AUTH C.FERRER-ORTA,A.ARIAS,R.PEREZ-LUQUE,C.ESCARMIS,E.DOMINGO, JRNL AUTH 2 N.VERDAGUER JRNL TITL SEQUENTIAL STRUCTURES PROVIDE INSIGHTS INTO THE FIDELITY OF JRNL TITL 2 RNA REPLICATION JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 9463 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17517631 JRNL DOI 10.1073/PNAS.0700518104 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.FERRER-ORTA,A.ARIAS,R.AGUDO,R.PEREZ-LUQUE,R.ESCARMIS, REMARK 1 AUTH 2 E.DOMINGO,N.VERDAGUER REMARK 1 TITL THE STRUCTURE OF A PROTEIN PRIMER-POLYMERASE COMPLEX IN THE REMARK 1 TITL 2 INITIATION OF GENOME REPLICATION REMARK 1 REF EMBO J. V. 25 880 2006 REMARK 1 REFN ISSN 0261-4189 REMARK 1 PMID 16456546 REMARK 1 DOI 10.1038/SJ.EMBOJ.7600971 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.FERRER-ORTA,A.ARIAS,C.ESCARMIS,N.VERDAGUER REMARK 1 TITL A COMPARISON OF VIRAL RNA-DEPENDENT RNA POLYMERASES REMARK 1 REF CURR.OPIN.STRUCT.BIOL. V. 16 27 2006 REMARK 1 REFN ISSN 0959-440X REMARK 1 PMID 16364629 REMARK 1 DOI 10.1016/J.SBI.2005.12.002 REMARK 1 REFERENCE 3 REMARK 1 AUTH C.FERRER-ORTA,A.ARIAS,R.PEREZ-LUQUE,C.ESCARMIS,E.DOMINGO, REMARK 1 AUTH 2 N.VERDAGUER REMARK 1 TITL STRUCTURE OF FOOT-AND-MOUTH DISEASE VIRUS RNA-DEPENDENT RNA REMARK 1 TITL 2 POLYMERASE AND ITS COMPLEX WITH A TEMPLATE-PRIMER RNA REMARK 1 REF J.BIOL.CHEM. V. 279 47212 2004 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 15294895 REMARK 1 DOI 10.1074/JBC.M405465200 REMARK 1 REFERENCE 4 REMARK 1 AUTH A.ARIAS,R.AGUDO,C.FERRER-ORTA,R.PEREZ-LUQUE,A.AIRAKSINEN, REMARK 1 AUTH 2 E.BROCCHI,E.DOMINGO,N.VERDAGUER,C.ESCARMIS REMARK 1 TITL MUTANT VIRAL POLYMERASE IN THE TRANSITION OF VIRUS TO ERROR REMARK 1 TITL 2 CATASTROPHE IDENTIFIES A CRITICAL SITE FOR RNA BINDING REMARK 1 REF J.MOL.BIOL. V. 353 1021 2005 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 16216271 REMARK 1 DOI 10.1016/J.JMB.2005.09.022 REMARK 2 REMARK 2 RESOLUTION. 2.81 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) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 11173 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 581 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) : 2.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 780 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 37 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3682 REMARK 3 NUCLEIC ACID ATOMS : 314 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 7 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03000 REMARK 3 B22 (A**2) : 1.03000 REMARK 3 B33 (A**2) : -1.54000 REMARK 3 B12 (A**2) : 0.51000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.523 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.389 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.511 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.914 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.876 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4150 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3537 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5706 ; 2.116 ; 2.047 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8223 ; 0.985 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 475 ; 7.977 ; 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): 627 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4438 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 813 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1241 ; 0.279 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4644 ; 0.255 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2339 ; 0.099 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 107 ; 0.196 ; 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): 19 ; 0.231 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 52 ; 0.282 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.218 ; 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): 2364 ; 0.794 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3785 ; 1.523 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1786 ; 2.110 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1921 ; 3.390 ; 4.500 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 : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2E9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000026403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11173 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.810 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1WNE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4K, 0.2M MAGNESIUM ACETATE, REMARK 280 0.1M SODIUM CACODILATE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 66.19000 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 33.09500 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 33.09500 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 66.19000 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: A, B, X 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 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 ASP X 5 CG OD1 OD2 REMARK 470 HIS X 14 CG ND1 CD2 CE1 NE2 REMARK 470 LYS X 18 CG CD CE NZ REMARK 470 LYS X 42 CG CD CE NZ REMARK 470 LYS X 103 CG CD CE NZ REMARK 470 GLU X 112 CG CD OE1 OE2 REMARK 470 ASP X 114 CG OD1 OD2 REMARK 470 THR X 115 OG1 CG2 REMARK 470 ARG X 127 CG CD NE CZ NH1 NH2 REMARK 470 GLU X 135 CG CD OE1 OE2 REMARK 470 ASN X 136 CG OD1 ND2 REMARK 470 GLU X 144 CG CD OE1 OE2 REMARK 470 GLU X 324 CG CD OE1 OE2 REMARK 470 LYS X 369 CG CD CE NZ REMARK 470 SER X 370 OG REMARK 470 ASP X 371 CG OD1 OD2 REMARK 470 LYS X 372 CG CD CE NZ REMARK 470 TYR X 394 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG X 417 CG CD NE CZ NH1 NH2 REMARK 470 LEU X 473 CG CD1 CD2 REMARK 470 HIS X 476 O 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 OP2 C B 920 O HOH B 503 2.05 REMARK 500 OE2 GLU X 351 NZ LYS X 354 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 GLU X 259 CD GLU X 259 OE2 -0.070 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 C A 902 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES REMARK 500 C A 902 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 A A 903 C3' - O3' - P ANGL. DEV. = -9.2 DEGREES REMARK 500 U A 904 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 G A 906 N9 - C1' - C2' ANGL. DEV. = -8.8 DEGREES REMARK 500 G A 906 O4' - C1' - N9 ANGL. DEV. = 8.7 DEGREES REMARK 500 C A 908 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 C A 910 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 C A 910 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 G B 915 N9 - C1' - C2' ANGL. DEV. = -8.5 DEGREES REMARK 500 G B 915 O4' - C1' - N9 ANGL. DEV. = 9.8 DEGREES REMARK 500 C B 918 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 C B 919 C6 - N1 - C2 ANGL. DEV. = 2.4 DEGREES REMARK 500 C B 920 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 C B 920 N1 - C1' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 C B 920 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ASP X 182 CB - CG - OD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP X 222 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP X 240 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG X 321 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ASP X 349 CB - CG - OD2 ANGL. DEV. = 7.8 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 ASP X 5 111.25 143.66 REMARK 500 THR X 6 142.45 -39.31 REMARK 500 VAL X 15 -65.68 -161.94 REMARK 500 MET X 16 99.09 -13.76 REMARK 500 PRO X 23 154.99 -43.73 REMARK 500 ASN X 31 66.33 38.61 REMARK 500 SER X 40 113.76 175.58 REMARK 500 ASN X 41 -8.48 -59.62 REMARK 500 ASP X 43 109.97 -14.84 REMARK 500 PRO X 44 -76.08 -43.31 REMARK 500 ARG X 45 -69.17 -20.71 REMARK 500 LEU X 46 127.53 -4.83 REMARK 500 ILE X 56 -30.73 -28.66 REMARK 500 HIS X 60 77.00 -102.35 REMARK 500 ASP X 63 54.27 -172.04 REMARK 500 THR X 64 115.40 -14.60 REMARK 500 SER X 67 157.65 -42.05 REMARK 500 PRO X 95 153.39 -49.33 REMARK 500 ILE X 98 -38.94 -36.02 REMARK 500 ALA X 101 -34.47 -36.13 REMARK 500 VAL X 105 -177.58 -60.27 REMARK 500 ALA X 116 152.47 -44.43 REMARK 500 PRO X 120 32.78 -88.35 REMARK 500 GLN X 124 22.47 -170.61 REMARK 500 ASP X 133 57.47 -91.90 REMARK 500 PHE X 134 -75.71 -7.26 REMARK 500 GLU X 151 -38.38 -36.85 REMARK 500 GLU X 154 52.05 -109.73 REMARK 500 THR X 161 137.60 -36.92 REMARK 500 LYS X 177 35.69 -99.11 REMARK 500 ASN X 207 157.04 -46.38 REMARK 500 PRO X 219 -5.77 -45.87 REMARK 500 TYR X 241 -130.47 -83.06 REMARK 500 SER X 242 113.66 151.59 REMARK 500 VAL X 279 -73.18 -73.92 REMARK 500 GLU X 286 -149.11 60.45 REMARK 500 SER X 298 109.86 -32.91 REMARK 500 SER X 301 141.91 -12.53 REMARK 500 ALA X 302 8.13 54.92 REMARK 500 HIS X 322 -45.40 -138.43 REMARK 500 ASP X 345 -78.22 -74.75 REMARK 500 TYR X 346 122.24 -21.14 REMARK 500 LYS X 354 -60.07 -25.50 REMARK 500 ASP X 371 -89.86 -108.81 REMARK 500 LYS X 372 -54.72 172.38 REMARK 500 HIS X 378 125.61 -31.07 REMARK 500 TYR X 394 -73.02 -43.46 REMARK 500 PRO X 445 -37.92 -35.42 REMARK 500 CYS X 467 87.98 -179.97 REMARK 500 GLU X 474 12.11 -62.82 REMARK 500 REMARK 500 THIS ENTRY HAS 51 RAMACHANDRAN OUTLIERS. 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 MG X 665 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP X 238 OD1 REMARK 620 2 ASP X 339 OD1 149.4 REMARK 620 3 HOH X 504 O 104.0 104.0 REMARK 620 4 HOH X 506 O 92.9 72.6 140.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 665 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RTP X 3832 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U09 RELATED DB: PDB REMARK 900 FOOT-AND-MOUTH DISEASE VIRUS RNA-DEPENDENT RNA POLYMERASE. REMARK 900 RELATED ID: 1WNE RELATED DB: PDB REMARK 900 FOOT AND MOUTH DISEASE VIRUS RNA-DEPENDENT RNA POLYMERASE IN REMARK 900 COMPLEX WITH A TEMPLATE-PRIMER RNA. REMARK 900 RELATED ID: 2D7S RELATED DB: PDB REMARK 900 FOOT AND MOUTH DISEASE VIRUS RNA-DEPENDENT RNA POLYMERASE IN REMARK 900 COMPLEX WITH PROTEIN-PRIMER VPG. REMARK 900 RELATED ID: 2F8E RELATED DB: PDB REMARK 900 FOOT AND MOUTH DISEASE VIRUS RNA-DEPENDENT RNA POLYMERASE IN REMARK 900 COMPLEX WITH PROTEIN-PRIMER VPG URIDILATED. REMARK 900 RELATED ID: 2E9T RELATED DB: PDB REMARK 900 RELATED ID: 2E9Z RELATED DB: PDB DBREF 2E9R X 1 470 UNP Q0QEE1 Q0QEE1_9PICO 1719 2188 DBREF 2E9R A 902 910 PDB 2E9R 2E9R 902 910 DBREF 2E9R B 915 920 PDB 2E9R 2E9R 915 920 SEQADV 2E9R ALA X 471 UNP Q0QEE1 CLONING ARTIFACT SEQADV 2E9R ALA X 472 UNP Q0QEE1 CLONING ARTIFACT SEQADV 2E9R LEU X 473 UNP Q0QEE1 CLONING ARTIFACT SEQADV 2E9R GLU X 474 UNP Q0QEE1 CLONING ARTIFACT SEQADV 2E9R HIS X 475 UNP Q0QEE1 CLONING ARTIFACT SEQADV 2E9R HIS X 476 UNP Q0QEE1 CLONING ARTIFACT SEQRES 1 A 9 C A U G G G C C C SEQRES 1 B 6 G G G C C C SEQRES 1 X 476 GLY LEU ILE VAL ASP THR ARG ASP VAL GLU GLU ARG VAL SEQRES 2 X 476 HIS VAL MET ARG LYS THR LYS LEU ALA PRO THR VAL ALA SEQRES 3 X 476 HIS GLY VAL PHE ASN PRO GLU PHE GLY PRO ALA ALA LEU SEQRES 4 X 476 SER ASN LYS ASP PRO ARG LEU ASN GLU GLY VAL VAL LEU SEQRES 5 X 476 ASP GLU VAL ILE PHE SER LYS HIS LYS GLY ASP THR LYS SEQRES 6 X 476 MET SER ALA GLU ASP LYS ALA LEU PHE ARG ARG CYS ALA SEQRES 7 X 476 ALA ASP TYR ALA SER ARG LEU HIS SER VAL LEU GLY THR SEQRES 8 X 476 ALA ASN ALA PRO LEU SER ILE TYR GLU ALA ILE LYS GLY SEQRES 9 X 476 VAL ASP GLY LEU ASP ALA MET GLU PRO ASP THR ALA PRO SEQRES 10 X 476 GLY LEU PRO TRP ALA LEU GLN GLY LYS ARG ARG GLY ALA SEQRES 11 X 476 LEU ILE ASP PHE GLU ASN GLY THR VAL GLY PRO GLU VAL SEQRES 12 X 476 GLU ALA ALA LEU LYS LEU MET GLU LYS ARG GLU TYR LYS SEQRES 13 X 476 PHE ALA CYS GLN THR PHE LEU LYS ASP GLU ILE ARG PRO SEQRES 14 X 476 MET GLU LYS VAL ARG ALA GLY LYS THR ARG ILE VAL ASP SEQRES 15 X 476 VAL LEU PRO VAL GLU HIS ILE LEU TYR THR ARG MET MET SEQRES 16 X 476 ILE GLY ARG PHE CYS ALA GLN MET HIS SER ASN ASN GLY SEQRES 17 X 476 PRO GLN ILE GLY SER ALA VAL GLY CYS ASN PRO ASP VAL SEQRES 18 X 476 ASP TRP GLN ARG PHE GLY THR HIS PHE ALA GLN TYR ARG SEQRES 19 X 476 ASN VAL TRP ASP VAL ASP TYR SER ALA PHE ASP ALA ASN SEQRES 20 X 476 HIS CYS SER ASP ALA MET ASN ILE MET PHE GLU GLU VAL SEQRES 21 X 476 PHE ARG THR GLU PHE GLY PHE HIS PRO ASN ALA GLU TRP SEQRES 22 X 476 ILE LEU LYS THR LEU VAL ASN THR GLU HIS ALA TYR GLU SEQRES 23 X 476 ASN LYS ARG ILE THR VAL GLU GLY GLY MET PRO SER GLY SEQRES 24 X 476 CYS SER ALA THR SER ILE ILE ASN THR ILE LEU ASN ASN SEQRES 25 X 476 ILE TYR VAL LEU TYR ALA LEU ARG ARG HIS TYR GLU GLY SEQRES 26 X 476 VAL GLU LEU ASP THR TYR THR MET ILE SER TYR GLY ASP SEQRES 27 X 476 ASP ILE VAL VAL ALA SER ASP TYR ASP LEU ASP PHE GLU SEQRES 28 X 476 ALA LEU LYS PRO HIS PHE LYS SER LEU GLY GLN THR ILE SEQRES 29 X 476 THR PRO ALA ASP LYS SER ASP LYS GLY PHE VAL LEU GLY SEQRES 30 X 476 HIS SER ILE THR ASP VAL THR PHE LEU LYS ARG HIS PHE SEQRES 31 X 476 HIS MET ASP TYR GLY THR GLY PHE TYR LYS PRO VAL MET SEQRES 32 X 476 ALA SER LYS THR LEU GLU ALA ILE LEU SER PHE ALA ARG SEQRES 33 X 476 ARG GLY THR ILE GLN GLU LYS LEU ILE SER VAL ALA GLY SEQRES 34 X 476 LEU ALA VAL HIS SER GLY PRO ASP GLU TYR ARG ARG LEU SEQRES 35 X 476 PHE GLU PRO PHE GLN GLY LEU PHE GLU ILE PRO SER TYR SEQRES 36 X 476 ARG SER LEU TYR LEU ARG TRP VAL ASN ALA VAL CYS GLY SEQRES 37 X 476 ASP ALA ALA ALA LEU GLU HIS HIS HET MG X 665 1 HET RTP X3832 29 HETNAM MG MAGNESIUM ION HETNAM RTP RIBAVIRIN TRIPHOSPHATE FORMUL 4 MG MG 2+ FORMUL 5 RTP C8 H15 N4 O14 P3 FORMUL 6 HOH *7(H2 O) HELIX 1 1 THR X 24 ASN X 31 1 8 HELIX 2 2 VAL X 51 ILE X 56 1 6 HELIX 3 3 SER X 67 GLY X 90 1 24 HELIX 4 4 SER X 97 GLY X 104 1 8 HELIX 5 5 ARG X 127 LEU X 131 5 5 HELIX 6 6 ASP X 133 GLY X 137 5 5 HELIX 7 7 GLY X 140 GLU X 151 1 12 HELIX 8 8 MET X 170 GLY X 176 1 7 HELIX 9 9 PRO X 185 ASN X 207 1 23 HELIX 10 10 GLY X 208 GLY X 212 5 5 HELIX 11 11 VAL X 221 ALA X 231 1 11 HELIX 12 12 ALA X 243 HIS X 248 5 6 HELIX 13 13 CYS X 249 PHE X 261 1 13 HELIX 14 14 PRO X 269 THR X 277 1 9 HELIX 15 15 ALA X 302 ARG X 321 1 20 HELIX 16 16 GLU X 327 TYR X 331 5 5 HELIX 17 17 ALA X 352 SER X 359 1 8 HELIX 18 18 TYR X 394 GLY X 397 5 4 HELIX 19 19 ALA X 404 LEU X 412 1 9 HELIX 20 20 THR X 419 VAL X 432 1 14 HELIX 21 21 SER X 434 LEU X 442 1 9 HELIX 22 22 PHE X 443 GLN X 447 5 5 HELIX 23 23 SER X 454 CYS X 467 1 14 HELIX 24 24 CYS X 467 ALA X 472 1 6 SHEET 1 A 3 LEU X 2 ILE X 3 0 SHEET 2 A 3 LYS X 288 GLU X 293 -1 O GLU X 293 N LEU X 2 SHEET 3 A 3 ARG X 7 ASP X 8 -1 N ARG X 7 O ARG X 289 SHEET 1 B 3 LEU X 2 ILE X 3 0 SHEET 2 B 3 LYS X 288 GLU X 293 -1 O GLU X 293 N LEU X 2 SHEET 3 B 3 THR X 281 TYR X 285 -1 N THR X 281 O VAL X 292 SHEET 1 C 2 LEU X 21 PRO X 23 0 SHEET 2 C 2 PHE X 414 ARG X 416 -1 O ALA X 415 N ALA X 22 SHEET 1 D 2 PHE X 34 PRO X 36 0 SHEET 2 D 2 ILE X 167 PRO X 169 -1 O ARG X 168 N GLY X 35 SHEET 1 E 2 GLN X 160 LEU X 163 0 SHEET 2 E 2 ILE X 180 VAL X 183 -1 O VAL X 183 N GLN X 160 SHEET 1 F 4 THR X 332 TYR X 336 0 SHEET 2 F 4 ASP X 339 SER X 344 -1 O VAL X 341 N ILE X 334 SHEET 3 F 4 ASN X 235 ASP X 240 -1 N ASN X 235 O SER X 344 SHEET 4 F 4 THR X 365 PRO X 366 -1 O THR X 365 N ASP X 240 SHEET 1 G 3 THR X 384 PHE X 385 0 SHEET 2 G 3 ARG X 388 MET X 392 -1 O ARG X 388 N PHE X 385 SHEET 3 G 3 TYR X 399 VAL X 402 -1 O LYS X 400 N HIS X 391 LINK OD1 ASP X 238 MG MG X 665 1555 1555 2.60 LINK OD1 ASP X 339 MG MG X 665 1555 1555 2.95 LINK O HOH X 504 MG MG X 665 1555 1555 2.68 LINK O HOH X 506 MG MG X 665 1555 1555 2.15 CISPEP 1 LEU X 119 PRO X 120 0 -15.82 SITE 1 AC1 6 ASP X 238 VAL X 239 ASP X 339 THR X 384 SITE 2 AC1 6 HOH X 504 HOH X 506 SITE 1 AC2 12 U A 904 G A 905 C B 920 ARG X 179 SITE 2 AC2 12 SER X 242 ALA X 243 PHE X 244 ASP X 245 SITE 3 AC2 12 SER X 298 GLY X 299 ASN X 307 ASP X 338 CRYST1 94.094 94.094 99.285 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 0.010628 0.006136 0.000000 0.00000 SCALE2 0.000000 0.012272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010072 0.00000