10 20 30 40 50 60 70 80 2QJ1 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE 06-JUL-07 2QJ1
TITLE CRYSTAL STRUCTURE OF INFECTIOUS BURSAL DISEASE VIRUS VP1 TITLE 2 POLYMERASE INCUBATED WITH AN OLIGOPEPTIDE MIMICKING THE TITLE 3 VP3 C-TERMINUS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: INFECTIOUS BURSAL DISEASE VIRUS VP1 POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: P2, VP1; COMPND 5 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; SOURCE 7 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 8 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: HIGH FIVE (TM) CELLS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: RECOMBINANT BACULOVIRUS SOURCE 12 (RBV)
KEYWDS INFECTIOUS BURSAL DISEASE VIRUS, IBDV, BIRNAVIRUS, KEYWDS 2 POLYMERASE, VP1, VP3, ACTIVATION, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.GARRIGA,A.NAVARRO,J.QUEROL-AUDI,F.ABAITUA,J.F.RODRIGUEZ, AUTHOR 2 N.VERDAGUER
REVDAT 2 24-FEB-09 2QJ1 1 VERSN REVDAT 1 27-NOV-07 2QJ1 0
JRNL AUTH D.GARRIGA,A.NAVARRO,J.QUEROL-AUDI,F.ABAITUA, JRNL AUTH 2 J.F.RODRIGUEZ,N.VERDAGUER JRNL TITL UNPRECEDENTED ACTIVATION MECHANISM OF A JRNL TITL 2 NON-CANONICAL RNA-DEPENDENT RNA POLYMERASE JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 3.48 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 20247 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) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1039 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) : 3.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1371 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5927 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.07000 REMARK 3 B12 (A**2) : -0.02000 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): 0.558 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.420 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 59.429 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.868 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.852 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6046 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8218 ; 1.023 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 757 ; 4.789 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 246 ;37.575 ;24.309 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1016 ;18.330 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;15.094 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 918 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4545 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2815 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4116 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 163 ; 0.116 ; 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): 34 ; 0.163 ; 0.200 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): 3898 ; 0.415 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6122 ; 0.685 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2462 ; 0.619 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2096 ; 1.036 ; 4.500 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 : 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 2QJ1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-07. REMARK 100 THE RCSB ID CODE IS RCSB043659.
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 : NULL 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20344 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.480 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.54000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: VP1 POLYMEASE APO FORM STRUCTURE (PDB CODE 2PUS) REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-12% PEG 3350, 0.3-0.5M LINO3, PH REMARK 280 6.5-8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
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 119.80867 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 239.61733 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 179.71300 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 299.52167 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 59.90433 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 119.80867 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 239.61733 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 299.52167 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 179.71300 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 59.90433 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 300 REMARK: THIS MOLECULE IS A MONOMER.
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 400 REMARK 400 COMPOUND REMARK 400 THE VP3 PEPTIDE WAS CRYSTALLIZED WITH THE VP1 PROTEIN, REMARK 400 BUT IT APPEARS POORLY ORDERED IN THE STRUCTURE OF THE REMARK 400 COMPLEX, AS ONLY A WEAK ELONGATED EXTRA DENSITY WAS REMARK 400 DETECTED. THIS DENSITY COULD BE INTERPRETED AS DUE TO REMARK 400 THE PRESENCE OF ABOUT FIVE AMINO ACIDS IN AN EXTENDED REMARK 400 CONFORMATION, BUT THE AUTHORS WERE NOT ABLE TO ASSIGN REMARK 400 ANY RESIDUE TO IT.
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 ASP A 238 REMARK 465 VAL A 239 REMARK 465 ASP A 240 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 ASP A 766 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 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 ILE A 88 CG1 CG2 CD1 REMARK 470 LEU A 93 CG CD1 CD2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 GLU A 217 CG CD OE1 OE2 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 VAL A 245 CG1 CG2 REMARK 470 GLU A 246 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 LYS A 606 CG CD CE NZ 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 SER A 610 OG 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 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 VAL A 804 CB CG1 CG2 REMARK 470 GLN A 805 CG CD OE1 NE2
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 GLY A 216 REMARK 475 GLU A 217 REMARK 475 ASP A 219
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 O VAL A 92 CD1 ILE A 271 1.82 REMARK 500 OG1 THR A 75 O LYS A 94 2.11 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 LEU A 93 N - CA - CB ANGL. DEV. = -19.4 DEGREES REMARK 500 TRP A 222 CB - CA - C ANGL. DEV. = -23.4 DEGREES REMARK 500 GLY A 420 N - CA - C ANGL. DEV. = -29.6 DEGREES REMARK 500 GLU A 421 CB - CA - C ANGL. DEV. = -18.9 DEGREES REMARK 500 GLU A 421 N - CA - CB ANGL. DEV. = 23.3 DEGREES REMARK 500 ALA A 422 N - CA - CB ANGL. DEV. = 9.6 DEGREES REMARK 500 SER A 610 CB - CA - C ANGL. DEV. = -27.9 DEGREES REMARK 500 SER A 610 N - CA - C ANGL. DEV. = 20.7 DEGREES REMARK 500 LYS A 611 CB - CA - C ANGL. DEV. = -15.0 DEGREES REMARK 500 LYS A 611 N - CA - CB ANGL. DEV. = -20.2 DEGREES REMARK 500 LYS A 611 N - CA - C ANGL. DEV. = -22.7 DEGREES REMARK 500 VAL A 612 N - CA - CB ANGL. DEV. = -22.8 DEGREES REMARK 500 ALA A 767 N - CA - C ANGL. DEV. = 21.5 DEGREES REMARK 500 ASP A 768 N - CA - C ANGL. DEV. = -19.3 DEGREES REMARK 500 VAL A 804 N - CA - C ANGL. DEV. = -21.1 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 LEU A 44 55.43 -101.09 REMARK 500 ASP A 76 42.18 -70.50 REMARK 500 GLN A 77 -59.31 -146.36 REMARK 500 LEU A 79 79.01 -119.37 REMARK 500 ALA A 91 -0.16 -140.25 REMARK 500 PRO A 95 -34.57 -31.48 REMARK 500 LYS A 120 72.79 -158.11 REMARK 500 ALA A 144 -134.24 53.63 REMARK 500 ASN A 145 97.10 67.33 REMARK 500 GLU A 217 -114.13 -120.58 REMARK 500 ASP A 219 117.91 139.16 REMARK 500 LYS A 220 -146.51 -113.58 REMARK 500 TRP A 222 0.49 83.77 REMARK 500 PRO A 250 107.46 -48.22 REMARK 500 PRO A 261 30.76 -95.28 REMARK 500 ALA A 293 -84.88 -91.44 REMARK 500 ASN A 358 32.11 -88.18 REMARK 500 PRO A 360 59.69 -91.62 REMARK 500 ARG A 379 5.36 57.02 REMARK 500 ALA A 401 -129.65 41.07 REMARK 500 LYS A 419 73.96 33.29 REMARK 500 GLU A 421 -7.01 81.99 REMARK 500 SER A 468 -112.85 -89.83 REMARK 500 MET A 473 -124.74 63.55 REMARK 500 MET A 507 39.36 -88.84 REMARK 500 GLN A 509 73.93 41.42 REMARK 500 LYS A 601 -177.33 -62.72 REMARK 500 GLU A 604 -143.69 53.38 REMARK 500 ASN A 605 121.98 -31.54 REMARK 500 SER A 607 -10.23 56.58 REMARK 500 LEU A 608 33.08 37.36 REMARK 500 VAL A 612 90.46 -15.92 REMARK 500 ILE A 614 -80.41 -6.75 REMARK 500 TRP A 632 -13.50 -48.18 REMARK 500 PHE A 657 133.08 -34.95 REMARK 500 PRO A 698 128.26 -31.44 REMARK 500 ASN A 727 85.18 -66.91 REMARK 500 ASP A 746 33.50 -77.11 REMARK 500 HIS A 758 -39.29 -39.17 REMARK 500 LYS A 759 -70.28 -58.29 REMARK 500 SER A 760 106.89 -53.75 REMARK 500 LYS A 761 -69.56 -125.85 REMARK 500 ASP A 768 155.88 172.36 REMARK 500 ALA A 790 -2.20 70.13 REMARK 500 VAL A 804 -144.69 55.29 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PUS RELATED DB: PDB REMARK 900 IBDV VP1 POLYMERASE, APO FORM
REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT RESIDUE AT POSITION 4 IS INDEED VALINE.
DBREF 2QJ1 A 1 845 UNP Q82629 Q82629_IBDV 1 845
SEQADV 2QJ1 GLY A -6 UNP Q82629 EXPRESSION TAG SEQADV 2QJ1 SER A -5 UNP Q82629 EXPRESSION TAG SEQADV 2QJ1 ARG A -4 UNP Q82629 EXPRESSION TAG SEQADV 2QJ1 SER A -3 UNP Q82629 EXPRESSION TAG SEQADV 2QJ1 THR A -2 UNP Q82629 EXPRESSION TAG SEQADV 2QJ1 VAL A -1 UNP Q82629 EXPRESSION TAG SEQADV 2QJ1 SER A 0 UNP Q82629 EXPRESSION TAG SEQADV 2QJ1 VAL A 4 UNP Q82629 ILE 4 SEE REMARK 999
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
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 PRO A 80 ALA A 83 5 4 HELIX 4 4 ASP A 127 VAL A 141 1 15 HELIX 5 5 ASN A 145 ASP A 161 1 17 HELIX 6 6 THR A 168 THR A 184 1 17 HELIX 7 7 ASP A 191 GLY A 196 5 6 HELIX 8 8 THR A 198 LEU A 210 1 13 HELIX 9 9 VAL A 228 MET A 232 5 5 HELIX 10 10 THR A 266 GLU A 269 5 4 HELIX 11 11 THR A 270 LYS A 290 1 21 HELIX 12 12 ASN A 299 TYR A 310 1 12 HELIX 13 13 TRP A 311 LEU A 313 5 3 HELIX 14 14 PRO A 341 ASN A 358 1 18 HELIX 15 15 PRO A 377 ARG A 379 5 3 HELIX 16 16 GLY A 380 ALA A 391 1 12 HELIX 17 17 THR A 425 ARG A 439 1 15 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 ALA A 488 MET A 507 1 20 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 GLY A 613 GLY A 630 1 18 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 LEU A 669 5 5 HELIX 30 30 PHE A 672 GLU A 677 5 6 HELIX 31 31 THR A 686 ASN A 694 1 9 HELIX 32 32 GLY A 712 LEU A 720 1 9 HELIX 33 33 ALA A 729 SER A 742 1 14 HELIX 34 34 ASP A 746 SER A 760 1 15 HELIX 35 35 TRP A 769 ALA A 783 1 15 HELIX 36 36 SER A 792 ALA A 800 1 9 HELIX 37 37 LEU A 801 ALA A 803 5 3
SHEET 1 A 2 LEU A 67 GLU A 74 0 SHEET 2 A 2 THR A 96 TYR A 106 -1 O TYR A 106 N LEU A 67 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 4 ASN A 336 SER A 339 0 SHEET 2 C 4 CYS A 315 PRO A 320 -1 N PHE A 319 O ILE A 337 SHEET 3 C 4 SER A 469 ILE A 472 1 O SER A 469 N GLY A 316 SHEET 4 C 4 LEU A 475 LYS A 478 -1 O ILE A 477 N CYS A 470 SHEET 1 D 4 LYS A 396 TYR A 400 0 SHEET 2 D 4 ASN A 403 HIS A 408 -1 O ASN A 403 N TYR A 400 SHEET 3 D 4 THR A 411 LEU A 417 -1 O ILE A 415 N ILE A 404 SHEET 4 D 4 PHE A 528 ILE A 534 -1 O ARG A 532 N SER A 414 SHEET 1 E 2 SER A 442 ASP A 443 0 SHEET 2 E 2 ASP A 446 PRO A 447 -1 O ASP A 446 N ASP A 443 SHEET 1 F 3 VAL A 566 LEU A 570 0 SHEET 2 F 3 TRP A 573 SER A 578 -1 O ALA A 575 N VAL A 566 SHEET 3 F 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 -3.84 CISPEP 2 ASP A 219 LYS A 220 0 0.09 CISPEP 3 LEU A 260 PRO A 261 0 1.50 CISPEP 4 GLU A 394 PRO A 395 0 0.28
CRYST1 121.913 121.913 359.426 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 0.008203 0.004736 0.000000 0.00000
SCALE2 0.000000 0.009472 0.000000 0.00000
SCALE3 0.000000 0.000000 0.002782 0.00000