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- PDB-1w9z: Structure of Bannavirus VP9 -

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Basic information

Entry
Database: PDB / ID: 1w9z
TitleStructure of Bannavirus VP9
ComponentsVP9
KeywordsVIRUS COAT PROTEIN / DSRNA VIRUS / OUTER CORE PROTEIN
Function / homologyRecoverin; domain 1 / Reoviridae VP9, N-terminal domain / Outer capsid protein VP9/VP10/VP11 / Outer capsid protein VP9, N-terminal / Reoviridae VP9 / Helix non-globular / Special / identical protein binding / VP9
Function and homology information
Biological speciesBANNA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.56 Å
AuthorsJaafar, F.M. / Attoui, H. / Bahar, M.W. / Siebold, C. / Sutton, G. / Mertens, P.P.C. / Micco, P. / Stuart, D.I. / Grimes, J.M. / Lamballerie, X.
CitationJournal: Structure / Year: 2005
Title: The Structure and Function of the Outer Coat Protein Vp9 of Banna Virus
Authors: Jaafar, F.M. / Attoui, H. / Bahar, M.W. / Siebold, C. / Sutton, G. / Mertens, P.P.C. / De Micco, P. / Stuart, D.I. / Grimes, J.M. / De Lamballerie, X.
History
DepositionOct 21, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP9
B: VP9
C: VP9


Theoretical massNumber of molelcules
Total (without water)91,6263
Polymers91,6263
Non-polymers00
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.386, 73.739, 95.722
Angle α, β, γ (deg.)90.00, 97.19, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.50038, -0.8658, 0.00259), (0.86563, -0.50034, -0.01841), (0.01724, -0.00697, 0.99983)-37.85624, 28.56519, 0.70023
2given(-0.49773, 0.8673, 0.00748), (-0.86733, -0.49773, -0.00173), (0.00222, -0.00735, 0.99997)-43.32686, -18.56732, 0.29084

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Components

#1: Protein VP9 / BANNAVIRUS VP9


Mass: 30542.080 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BANNA VIRUS / Strain: BAV-CH / Plasmid: PGEX-4T-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): BL-CODONPLUS(DE3)-RP-X / References: UniProt: Q9YWN5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.07 % / Description: NO NATIVE DATA WERE COLLECTED
Crystal growpH: 8
Details: 0.1 M HEPES-NA, PH 7.5, 20% (W/V) POLYETHYLENE GLYCOL 4000, 10% (V/V) ISO-PROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.87, 0.97
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 8, 2003 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
20.971
ReflectionResolution: 2.55→30 Å / Num. obs: 27995 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.6
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC18.3refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.56→94.92 Å / SU B: 21.923 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.743 / ESU R Free: 0.309
RfactorNum. reflection% reflectionSelection details
Rfree0.24844 1417 5.1 %RANDOM
Rwork0.18317 ---
obs0.18646 26540 98.71 %-
Displacement parametersBiso mean: 19.105 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å2-0.77 Å2
2---1.72 Å20 Å2
3---2.88 Å2
Refinement stepCycle: LAST / Resolution: 2.56→94.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5809 0 0 200 6009

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