+Open data
-Basic information
Entry | Database: PDB / ID: 3vne | ||||||
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Title | Structure of the ebolavirus protein VP24 from Sudan | ||||||
Components | Membrane-associated protein VP24 | ||||||
Keywords | VIRAL PROTEIN / ebolavirus / interferon antagonist / VP24 / STAT1 / Zaire / Sudan / Reston / VP35 / karyopherin alpha / IFN response pathway | ||||||
Function / homology | Function and homology information host cell endomembrane system / endomembrane system / virus-mediated perturbation of host defense response / host cell plasma membrane / virion membrane / structural molecule activity / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Sudan ebolavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zhang, A.P.P. | ||||||
Citation | Journal: Plos Pathog. / Year: 2012 Title: The ebola virus interferon antagonist VP24 directly binds STAT1 and has a novel, pyramidal fold Authors: Zhang, A.P.P. / Bornholdt, Z.A. / Liu, T. / Abelson, D.M. / Lee, D.E. / Li, S. / Woods Jr., V.L. / Saphire, E.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vne.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vne.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/3vne ftp://data.pdbj.org/pub/pdb/validation_reports/vn/3vne | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25379.445 Da / Num. of mol.: 1 / Fragment: UNP residues 9-232 / Mutation: V22A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sudan ebolavirus / Gene: VP24 / Production host: Escherichia coli (E. coli) / References: UniProt: B0LPM0, UniProt: Q5XX02*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.44 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M HEPES, 0.1M MgCl, 8% PEG 550mme, pH 7.5, vapor diffusion, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2010 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.6 Å / Num. all: 19597 / Num. obs: 19519 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 43.62 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.4 |
Reflection shell | Highest resolution: 2 Å / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→33.569 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7373 / SU ML: 0.38 / σ(F): 0 / Phase error: 31.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.299 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.86 Å2 / Biso mean: 53.0937 Å2 / Biso min: 24.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.569 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -22.4122 Å / Origin y: -4.6759 Å / Origin z: -4.8694 Å
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Refinement TLS group | Selection details: (chain A and resid 9:232) |