HEADER TRANSFERASE 07-SEP-07 2R72 TITLE CRYSTAL STRUCTURE OF INFECTIOUS BURSAL DISEASE VIRUS VP1 POLYMERASE, TITLE 2 INCUBATED WITH MG2+ ION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: INFECTIOUS BURSAL DISEASE VIRUS VP1 POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFECTIOUS BURSAL DISEASE VIRUS; SOURCE 3 ORGANISM_COMMON: GUMBORO VIRUS; SOURCE 4 ORGANISM_TAXID: 10995; SOURCE 5 STRAIN: SOROA; SOURCE 6 GENE: VP1 POLYMERASE (SEGMENT B); SOURCE 7 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 8 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 10 EXPRESSION_SYSTEM_CELL: HIGHFIVE CELLS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS IBDV, INFECTIOUS BURSAL DISEASE VIRUS, BIRNAVIRUS, VP1, POLYMERASE, KEYWDS 2 MAGNESIUM, MG, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.GARRIGA,A.NAVARRO,J.QUEROL-AUDI,F.ABAITUA,J.F.RODRIGUEZ,N.VERDAGUER REVDAT 5 30-AUG-23 2R72 1 REMARK REVDAT 4 13-JUL-11 2R72 1 VERSN REVDAT 3 24-FEB-09 2R72 1 VERSN REVDAT 2 22-JAN-08 2R72 1 JRNL REVDAT 1 27-NOV-07 2R72 0 JRNL AUTH D.GARRIGA,A.NAVARRO,J.QUEROL-AUDI,F.ABAITUA,J.F.RODRIGUEZ, JRNL AUTH 2 N.VERDAGUER JRNL TITL ACTIVATION MECHANISM OF A NONCANONICAL RNA-DEPENDENT RNA JRNL TITL 2 POLYMERASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 20540 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 18077388 JRNL DOI 10.1073/PNAS.0704447104 REMARK 2 REMARK 2 RESOLUTION. 3.15 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) : 3.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 27545 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1393 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) : 3.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1846 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 112 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5915 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.34000 REMARK 3 B22 (A**2) : -0.34000 REMARK 3 B33 (A**2) : 0.51000 REMARK 3 B12 (A**2) : -0.17000 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): 1.048 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.362 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.277 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 35.261 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.894 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6053 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8231 ; 0.962 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 760 ; 4.716 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 245 ;36.265 ;24.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1014 ;16.509 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;18.041 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 920 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4557 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2734 ; 0.181 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4184 ; 0.297 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 123 ; 0.104 ; 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): 30 ; 0.142 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.045 ; 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): 3909 ; 0.279 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6139 ; 0.504 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2456 ; 0.447 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2092 ; 0.807 ; 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 : 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 27 A 803 REMARK 3 ORIGIN FOR THE GROUP (A): -28.7939 -36.4306 111.5113 REMARK 3 T TENSOR REMARK 3 T11: -0.1003 T22: -0.2445 REMARK 3 T33: -0.1129 T12: 0.0865 REMARK 3 T13: 0.1587 T23: 0.1308 REMARK 3 L TENSOR REMARK 3 L11: 1.8178 L22: 1.2136 REMARK 3 L33: 1.4871 L12: -0.6313 REMARK 3 L13: -1.0612 L23: 0.3366 REMARK 3 S TENSOR REMARK 3 S11: 0.0710 S12: 0.0715 S13: 0.1311 REMARK 3 S21: -0.2682 S22: -0.0248 S23: -0.2829 REMARK 3 S31: -0.1940 S32: 0.1837 S33: -0.0462 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 2R72 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000044505. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27660 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.150 REMARK 200 RESOLUTION RANGE LOW (A) : 36.664 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : 0.12100 REMARK 200 FOR THE DATA SET : 5.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.35600 REMARK 200 R SYM FOR SHELL (I) : 0.35600 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 2PUS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 0.4M LINO3, 0.1M MES, PH REMARK 280 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 118.08500 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 236.17000 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 177.12750 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 295.21250 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 59.04250 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 118.08500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 236.17000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 295.21250 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 177.12750 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 59.04250 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 GLY A -6 REMARK 465 SER A -5 REMARK 465 ARG A -4 REMARK 465 SER A -3 REMARK 465 THR A -2 REMARK 465 VAL A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 VAL A 4 REMARK 465 PHE A 5 REMARK 465 ASN A 6 REMARK 465 SER A 7 REMARK 465 PRO A 8 REMARK 465 GLN A 9 REMARK 465 ALA A 10 REMARK 465 ARG A 11 REMARK 465 SER A 12 REMARK 465 THR A 13 REMARK 465 ILE A 14 REMARK 465 SER A 15 REMARK 465 ALA A 16 REMARK 465 ALA A 17 REMARK 465 PHE A 18 REMARK 465 GLY A 19 REMARK 465 ILE A 20 REMARK 465 LYS A 21 REMARK 465 PRO A 22 REMARK 465 THR A 23 REMARK 465 ALA A 24 REMARK 465 GLY A 25 REMARK 465 GLN A 26 REMARK 465 GLU A 89 REMARK 465 GLY A 90 REMARK 465 ALA A 91 REMARK 465 VAL A 92 REMARK 465 GLU A 217 REMARK 465 GLY A 241 REMARK 465 ASP A 242 REMARK 465 PHE A 243 REMARK 465 GLU A 244 REMARK 465 ASP A 763 REMARK 465 ASP A 764 REMARK 465 PRO A 765 REMARK 465 VAL A 804 REMARK 465 GLN A 805 REMARK 465 SER A 806 REMARK 465 THR A 807 REMARK 465 SER A 808 REMARK 465 VAL A 809 REMARK 465 TYR A 810 REMARK 465 THR A 811 REMARK 465 PRO A 812 REMARK 465 LYS A 813 REMARK 465 TYR A 814 REMARK 465 PRO A 815 REMARK 465 GLU A 816 REMARK 465 VAL A 817 REMARK 465 LYS A 818 REMARK 465 ASN A 819 REMARK 465 PRO A 820 REMARK 465 GLN A 821 REMARK 465 THR A 822 REMARK 465 ALA A 823 REMARK 465 SER A 824 REMARK 465 ASN A 825 REMARK 465 PRO A 826 REMARK 465 VAL A 827 REMARK 465 VAL A 828 REMARK 465 GLY A 829 REMARK 465 LEU A 830 REMARK 465 HIS A 831 REMARK 465 LEU A 832 REMARK 465 PRO A 833 REMARK 465 ALA A 834 REMARK 465 LYS A 835 REMARK 465 ARG A 836 REMARK 465 ALA A 837 REMARK 465 THR A 838 REMARK 465 GLY A 839 REMARK 465 VAL A 840 REMARK 465 GLN A 841 REMARK 465 ALA A 842 REMARK 465 ALA A 843 REMARK 465 LEU A 844 REMARK 465 LEU A 845 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 A 27 CG OD1 OD2 REMARK 470 VAL A 28 CG1 CG2 REMARK 470 GLU A 74 CG CD OE1 OE2 REMARK 470 ARG A 86 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 87 CG CD OE1 NE2 REMARK 470 LEU A 93 CG CD1 CD2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 ASP A 218 CG OD1 OD2 REMARK 470 ASP A 219 CG OD1 OD2 REMARK 470 LYS A 220 CG CD CE NZ REMARK 470 THR A 236 OG1 CG2 REMARK 470 ASP A 240 CG OD1 OD2 REMARK 470 VAL A 245 CG1 CG2 REMARK 470 GLU A 246 CG CD OE1 OE2 REMARK 470 GLU A 367 CG CD OE1 OE2 REMARK 470 VAL A 603 CG1 CG2 REMARK 470 GLU A 604 CG CD OE1 OE2 REMARK 470 ASN A 605 CG OD1 ND2 REMARK 470 SER A 607 OG REMARK 470 LEU A 608 CG CD1 CD2 REMARK 470 LYS A 609 CG CD CE NZ REMARK 470 LYS A 611 CG CD CE NZ REMARK 470 VAL A 612 CG1 CG2 REMARK 470 GLU A 615 CG CD OE1 OE2 REMARK 470 GLU A 653 CG CD OE1 OE2 REMARK 470 GLU A 661 CG CD OE1 OE2 REMARK 470 ASN A 680 CG OD1 ND2 REMARK 470 LYS A 761 CG CD CE NZ REMARK 470 PRO A 762 CG CD REMARK 470 ASP A 766 CG OD1 OD2 REMARK 470 GLU A 771 CG CD OE1 OE2 REMARK 470 GLU A 781 CG CD OE1 OE2 REMARK 470 ASP A 784 CG OD1 OD2 REMARK 470 LYS A 788 CG CD CE NZ 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 GLU A 30 105.32 33.37 REMARK 500 TRP A 84 8.37 -62.27 REMARK 500 MET A 85 36.10 -74.09 REMARK 500 LYS A 94 119.96 85.52 REMARK 500 GLN A 104 110.30 82.22 REMARK 500 ALA A 144 -136.87 46.21 REMARK 500 ASN A 145 100.34 72.53 REMARK 500 LEU A 210 66.35 -150.71 REMARK 500 ASP A 219 -24.58 63.96 REMARK 500 PRO A 221 78.64 -104.68 REMARK 500 VAL A 239 103.82 68.18 REMARK 500 PRO A 261 39.82 -93.69 REMARK 500 SER A 298 38.10 -77.76 REMARK 500 ASN A 365 -1.38 -140.58 REMARK 500 GLU A 394 147.01 -174.89 REMARK 500 ALA A 401 -116.50 45.69 REMARK 500 MET A 448 38.30 -96.59 REMARK 500 SER A 468 -126.12 -89.95 REMARK 500 ILE A 472 -97.21 -86.44 REMARK 500 MET A 473 -102.76 -78.82 REMARK 500 ASN A 486 -33.83 -150.06 REMARK 500 GLN A 509 70.89 54.90 REMARK 500 SER A 554 86.22 -150.14 REMARK 500 ASP A 589 128.39 -37.68 REMARK 500 GLU A 604 88.62 76.07 REMARK 500 ASN A 605 119.58 66.50 REMARK 500 SER A 607 -133.96 -79.56 REMARK 500 LYS A 609 92.78 -60.37 REMARK 500 SER A 610 -161.38 59.10 REMARK 500 LYS A 611 -78.62 -151.49 REMARK 500 THR A 684 -44.96 -133.90 REMARK 500 ASP A 746 32.13 -98.34 REMARK 500 ALA A 767 93.00 -53.68 REMARK 500 ASP A 768 134.16 75.80 REMARK 500 ALA A 790 -7.27 67.15 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 MG A 846 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 847 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 848 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PUS RELATED DB: PDB REMARK 900 IBDV VP1 STRUCTURE, APO FORM REMARK 900 RELATED ID: 2R70 RELATED DB: PDB REMARK 900 IBDV VP1 STRUCTURE, COCRYSTALLIZED WITH A PEPTIDE MIMICKING VP3 C- REMARK 900 TERMINUS REMARK 900 RELATED ID: 2QJ1 RELATED DB: PDB REMARK 900 IBDV VP1 STRUCTURE, CRYSTAL SOAKED WITH A PEPTIDE MIMICKING VP3 C- REMARK 900 TERMINUS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT DATABASE AT REMARK 999 THE TIME OF PROCESSING. DBREF 2R72 A 1 845 UNP Q9Q6Q5 RDRP_IBDV 1 845 SEQRES 1 A 852 GLY SER ARG SER THR VAL SER MET SER ASP VAL PHE ASN SEQRES 2 A 852 SER PRO GLN ALA ARG SER THR ILE SER ALA ALA PHE GLY SEQRES 3 A 852 ILE LYS PRO THR ALA GLY GLN ASP VAL GLU GLU LEU LEU SEQRES 4 A 852 ILE PRO LYS VAL TRP VAL PRO PRO GLU ASP PRO LEU ALA SEQRES 5 A 852 SER PRO SER ARG LEU ALA LYS PHE LEU ARG GLU ASN GLY SEQRES 6 A 852 TYR LYS VAL LEU GLN PRO ARG SER LEU PRO GLU ASN GLU SEQRES 7 A 852 GLU TYR GLU THR ASP GLN ILE LEU PRO ASP LEU ALA TRP SEQRES 8 A 852 MET ARG GLN ILE GLU GLY ALA VAL LEU LYS PRO THR LEU SEQRES 9 A 852 SER LEU PRO ILE GLY ASP GLN GLU TYR PHE PRO LYS TYR SEQRES 10 A 852 TYR PRO THR HIS ARG PRO SER LYS GLU LYS PRO ASN ALA SEQRES 11 A 852 TYR PRO PRO ASP ILE ALA LEU LEU LYS GLN MET ILE TYR SEQRES 12 A 852 LEU PHE LEU GLN VAL PRO GLU ALA ASN GLU GLY LEU LYS SEQRES 13 A 852 ASP GLU VAL THR LEU LEU THR GLN ASN ILE ARG ASP LYS SEQRES 14 A 852 ALA TYR GLY SER GLY THR TYR MET GLY GLN ALA ASN ARG SEQRES 15 A 852 LEU VAL ALA MET LYS GLU VAL ALA THR GLY ARG ASN PRO SEQRES 16 A 852 ASN LYS ASP PRO LEU LYS LEU GLY TYR THR PHE GLU SER SEQRES 17 A 852 ILE ALA GLN LEU LEU ASP ILE THR LEU PRO VAL GLY PRO SEQRES 18 A 852 PRO GLY GLU ASP ASP LYS PRO TRP VAL PRO LEU THR ARG SEQRES 19 A 852 VAL PRO SER ARG MET LEU VAL LEU THR GLY ASP VAL ASP SEQRES 20 A 852 GLY ASP PHE GLU VAL GLU ASP TYR LEU PRO LYS ILE ASN SEQRES 21 A 852 LEU LYS SER SER SER GLY LEU PRO TYR VAL GLY ARG THR SEQRES 22 A 852 LYS GLY GLU THR ILE GLY GLU MET ILE ALA ILE SER ASN SEQRES 23 A 852 GLN PHE LEU ARG GLU LEU SER THR LEU LEU LYS GLN GLY SEQRES 24 A 852 ALA GLY THR LYS GLY SER ASN LYS LYS LYS LEU LEU SER SEQRES 25 A 852 MET LEU SER ASP TYR TRP TYR LEU SER CYS GLY LEU LEU SEQRES 26 A 852 PHE PRO LYS ALA GLU ARG TYR ASP LYS SER THR TRP LEU SEQRES 27 A 852 THR LYS THR ARG ASN ILE TRP SER ALA PRO SER PRO THR SEQRES 28 A 852 HIS LEU MET ILE SER MET ILE THR TRP PRO VAL MET SER SEQRES 29 A 852 ASN SER PRO ASN ASN VAL LEU ASN ILE GLU GLY CYS PRO SEQRES 30 A 852 SER LEU TYR LYS PHE ASN PRO PHE ARG GLY GLY LEU ASN SEQRES 31 A 852 ARG ILE VAL GLU TRP ILE LEU ALA PRO GLU GLU PRO LYS SEQRES 32 A 852 ALA LEU VAL TYR ALA ASP ASN ILE TYR ILE VAL HIS SER SEQRES 33 A 852 ASN THR TRP TYR SER ILE ASP LEU GLU LYS GLY GLU ALA SEQRES 34 A 852 ASN CYS THR ARG GLN HIS MET GLN ALA ALA MET TYR TYR SEQRES 35 A 852 ILE LEU THR ARG GLY TRP SER ASP ASN GLY ASP PRO MET SEQRES 36 A 852 PHE ASN GLN THR TRP ALA THR PHE ALA MET ASN ILE ALA SEQRES 37 A 852 PRO ALA LEU VAL VAL ASP SER SER CYS LEU ILE MET ASN SEQRES 38 A 852 LEU GLN ILE LYS THR TYR GLY GLN GLY SER GLY ASN ALA SEQRES 39 A 852 ALA THR PHE ILE ASN ASN HIS LEU LEU SER THR LEU VAL SEQRES 40 A 852 LEU ASP GLN TRP ASN LEU MET ARG GLN PRO ARG PRO ASP SEQRES 41 A 852 SER GLU GLU PHE LYS SER ILE GLU ASP LYS LEU GLY ILE SEQRES 42 A 852 ASN PHE LYS ILE GLU ARG SER ILE ASP ASP ILE ARG GLY SEQRES 43 A 852 LYS LEU ARG GLN LEU VAL LEU LEU ALA GLN PRO GLY TYR SEQRES 44 A 852 LEU SER GLY GLY VAL GLU PRO GLU GLN SER SER PRO THR SEQRES 45 A 852 VAL GLU LEU ASP LEU LEU GLY TRP SER ALA THR TYR SER SEQRES 46 A 852 LYS ASP LEU GLY ILE TYR VAL PRO VAL LEU ASP LYS GLU SEQRES 47 A 852 ARG LEU PHE CYS SER ALA ALA TYR PRO LYS GLY VAL GLU SEQRES 48 A 852 ASN LYS SER LEU LYS SER LYS VAL GLY ILE GLU GLN ALA SEQRES 49 A 852 TYR LYS VAL VAL ARG TYR GLU ALA LEU ARG LEU VAL GLY SEQRES 50 A 852 GLY TRP ASN TYR PRO LEU LEU ASN LYS ALA CYS LYS ASN SEQRES 51 A 852 ASN ALA GLY ALA ALA ARG ARG HIS LEU GLU ALA LYS GLY SEQRES 52 A 852 PHE PRO LEU ASP GLU PHE LEU ALA GLU TRP SER GLU LEU SEQRES 53 A 852 SER GLU PHE GLY GLU ALA PHE GLU GLY PHE ASN ILE LYS SEQRES 54 A 852 LEU THR VAL THR SER GLU SER LEU ALA GLU LEU ASN LYS SEQRES 55 A 852 PRO VAL PRO PRO LYS PRO PRO ASN VAL ASN ARG PRO VAL SEQRES 56 A 852 ASN THR GLY GLY LEU LYS ALA VAL SER ASN ALA LEU LYS SEQRES 57 A 852 THR GLY ARG TYR ARG ASN GLU ALA GLY LEU SER GLY LEU SEQRES 58 A 852 VAL LEU LEU ALA THR ALA ARG SER ARG LEU GLN ASP ALA SEQRES 59 A 852 VAL LYS ALA LYS ALA GLU ALA GLU LYS LEU HIS LYS SER SEQRES 60 A 852 LYS PRO ASP ASP PRO ASP ALA ASP TRP PHE GLU ARG SER SEQRES 61 A 852 GLU THR LEU SER ASP LEU LEU GLU LYS ALA ASP ILE ALA SEQRES 62 A 852 SER LYS VAL ALA HIS SER ALA LEU VAL GLU THR SER ASP SEQRES 63 A 852 ALA LEU GLU ALA VAL GLN SER THR SER VAL TYR THR PRO SEQRES 64 A 852 LYS TYR PRO GLU VAL LYS ASN PRO GLN THR ALA SER ASN SEQRES 65 A 852 PRO VAL VAL GLY LEU HIS LEU PRO ALA LYS ARG ALA THR SEQRES 66 A 852 GLY VAL GLN ALA ALA LEU LEU HET MG A 846 1 HET MG A 847 1 HET MG A 848 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 3(MG 2+) FORMUL 5 HOH *3(H2 O) HELIX 1 1 SER A 46 ASN A 57 1 12 HELIX 2 2 THR A 75 LEU A 79 1 5 HELIX 3 3 ASP A 127 VAL A 141 1 15 HELIX 4 4 ASN A 145 ASP A 161 1 17 HELIX 5 5 THR A 168 GLY A 185 1 18 HELIX 6 6 ASP A 191 GLY A 196 5 6 HELIX 7 7 THR A 198 LEU A 210 1 13 HELIX 8 8 VAL A 228 ARG A 231 5 4 HELIX 9 9 THR A 270 GLN A 291 1 22 HELIX 10 10 GLY A 294 SER A 298 5 5 HELIX 11 11 ASN A 299 TYR A 310 1 12 HELIX 12 12 TRP A 311 LEU A 313 5 3 HELIX 13 13 SER A 328 TRP A 330 5 3 HELIX 14 14 PRO A 341 SER A 357 1 17 HELIX 15 15 GLY A 380 ALA A 391 1 12 HELIX 16 16 GLY A 420 CYS A 424 5 5 HELIX 17 17 THR A 425 GLY A 440 1 16 HELIX 18 18 ASN A 450 ILE A 460 1 11 HELIX 19 19 ILE A 460 VAL A 466 1 7 HELIX 20 20 THR A 489 MET A 507 1 19 HELIX 21 21 SER A 514 SER A 519 1 6 HELIX 22 22 SER A 519 GLY A 525 1 7 HELIX 23 23 ASP A 536 LEU A 547 1 12 HELIX 24 24 ASP A 589 TYR A 599 1 11 HELIX 25 25 LYS A 611 GLY A 630 1 20 HELIX 26 26 GLY A 631 ASN A 633 5 3 HELIX 27 27 TYR A 634 GLY A 656 1 23 HELIX 28 28 PRO A 658 LEU A 663 1 6 HELIX 29 29 GLU A 665 SER A 670 1 6 HELIX 30 30 PHE A 672 GLU A 677 5 6 HELIX 31 31 THR A 686 LYS A 695 1 10 HELIX 32 32 GLY A 712 THR A 722 1 11 HELIX 33 33 GLY A 730 SER A 742 1 13 HELIX 34 34 ASP A 746 LYS A 759 1 14 HELIX 35 35 TRP A 769 ALA A 783 1 15 HELIX 36 36 SER A 792 LEU A 801 1 10 SHEET 1 A 2 LEU A 67 GLU A 74 0 SHEET 2 A 2 THR A 96 TYR A 106 -1 O LEU A 97 N TYR A 73 SHEET 1 B 2 LYS A 162 GLY A 165 0 SHEET 2 B 2 GLU A 323 ASP A 326 -1 O TYR A 325 N ALA A 163 SHEET 1 C 2 LEU A 233 VAL A 234 0 SHEET 2 C 2 GLU A 246 ASP A 247 -1 O GLU A 246 N VAL A 234 SHEET 1 D 2 SER A 257 GLY A 259 0 SHEET 2 D 2 TYR A 262 THR A 266 -1 O ARG A 265 N SER A 258 SHEET 1 E 4 ASN A 336 SER A 339 0 SHEET 2 E 4 CYS A 315 PRO A 320 -1 N PHE A 319 O ILE A 337 SHEET 3 E 4 SER A 469 LEU A 471 1 O LEU A 471 N GLY A 316 SHEET 4 E 4 GLN A 476 LYS A 478 -1 O ILE A 477 N CYS A 470 SHEET 1 F 4 LYS A 396 TYR A 400 0 SHEET 2 F 4 ASN A 403 HIS A 408 -1 O TYR A 405 N LEU A 398 SHEET 3 F 4 THR A 411 LEU A 417 -1 O ILE A 415 N ILE A 404 SHEET 4 F 4 PHE A 528 ASP A 535 -1 O ARG A 532 N SER A 414 SHEET 1 G 2 SER A 442 ASP A 443 0 SHEET 2 G 2 ASP A 446 PRO A 447 -1 O ASP A 446 N ASP A 443 SHEET 1 H 3 VAL A 566 LEU A 570 0 SHEET 2 H 3 TRP A 573 SER A 578 -1 O TRP A 573 N LEU A 570 SHEET 3 H 3 ILE A 583 LEU A 588 -1 O VAL A 585 N THR A 576 CISPEP 1 ARG A 115 PRO A 116 0 -7.84 CISPEP 2 LEU A 260 PRO A 261 0 -1.41 CISPEP 3 GLU A 394 PRO A 395 0 1.06 SITE 1 AC1 4 ASP A 402 LEU A 417 LYS A 419 GLY A 420 SITE 1 AC2 3 ALA A 401 ASP A 402 ASN A 493 SITE 1 AC3 5 ASN A 403 TYR A 405 SER A 414 ILE A 415 SITE 2 AC3 5 ASP A 416 CRYST1 122.838 122.838 354.255 90.00 90.00 120.00 P 61 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008141 0.004700 0.000000 0.00000 SCALE2 0.000000 0.009400 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002823 0.00000