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Yorodumi- PDB-5ej0: The vaccinia virus H3 envelope protein, a major target of neutral... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ej0 | ||||||
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Title | The vaccinia virus H3 envelope protein, a major target of neutralizing antibodies, exhibits a glycosyltransferase fold and binds UDP-Glucose | ||||||
Components | Envelope protein H3 | ||||||
Keywords | VIRAL PROTEIN / H3 / vaccinia virus / poxvirus / glycosyl transferase | ||||||
Function / homology | Function and homology information membrane => GO:0016020 / symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane Similarity search - Function | ||||||
Biological species | Vaccinia virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Singh, K. / Gittis, A.G. / Gitti, R.K. / Ostazesky, S.A. / Su, H.P. / Garboczi, D.N. | ||||||
Citation | Journal: J.Virol. / Year: 2016 Title: The Vaccinia Virus H3 Envelope Protein, a Major Target of Neutralizing Antibodies, Exhibits a Glycosyltransferase Fold and Binds UDP-Glucose. Authors: Singh, K. / Gittis, A.G. / Gitti, R.K. / Ostazeski, S.A. / Su, H.P. / Garboczi, D.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ej0.cif.gz | 64.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ej0.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ej0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/5ej0 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5ej0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27486.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus (strain Western Reserve) Strain: Western Reserve / Gene: VACWR101, H3L / Plasmid: pNAN / Production host: Escherichia coli (E. coli) / References: UniProt: P07240 |
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-Non-polymers , 10 types, 116 molecules
#2: Chemical | ChemComp-DHL / | ||||||||||||||||
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#3: Chemical | ChemComp-PG0 / #4: Chemical | #5: Chemical | ChemComp-POL / | #6: Chemical | #7: Chemical | ChemComp-EDO / #8: Chemical | #9: Chemical | ChemComp-MOH / #10: Chemical | ChemComp-MG / | #11: Water | ChemComp-HOH / | |
-Details
Sequence details | AUTHORS HAVE INDICATED THAT THE SEQUENCE IN THE UNPROT ENTRY P07240 IS INCORRECT |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 100 mM citric acid, 10-20% PEG 6000, 5% 1,3-propanediol and mixture of low molecular mass alcohols |
-Data collection
Diffraction | Mean temperature: 95 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: Jul 28, 2005 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.22 Å / Num. obs: 21213 / % possible obs: 99.81 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.79 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.54 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→49.216 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.01 Å2 / Biso mean: 33.3324 Å2 / Biso min: 11.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→49.216 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: 12
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