+Open data
-Basic information
Entry | Database: PDB / ID: 6a9s | |||||||||
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Title | The crystal structure of vaccinia virus A26 (residues 1-397) | |||||||||
Components | Protein A26 | |||||||||
Keywords | VIRAL PROTEIN / Vaccinia virus / virus entry / acid sensitive | |||||||||
Function / homology | Orthopoxvirus A26L/A30L / Orthopoxvirus A26L/A30L protein / Chordopoxvirus fusion protein/multifunctional envelope protein A27 / Chordopoxvirus multifunctional envelope protein A27 / fusion of virus membrane with host plasma membrane / viral envelope / virion membrane / membrane / Envelop protein OPG153 Function and homology information | |||||||||
Biological species | Vaccinia virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.18 Å | |||||||||
Authors | Wang, H.C. / Ko, T.Z. / Luo, Y.C. / Liao, Y.T. / Chang, W. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: Plos Pathog. / Year: 2019 Title: Vaccinia viral A26 protein is a fusion suppressor of mature virus and triggers membrane fusion through conformational change at low pH. Authors: Chang, H.W. / Yang, C.H. / Luo, Y.C. / Su, B.G. / Cheng, H.Y. / Tung, S.Y. / Carillo, K.J.D. / Liao, Y.T. / Tzou, D.M. / Wang, H.C. / Chang, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a9s.cif.gz | 183.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a9s.ent.gz | 151.4 KB | Display | PDB format |
PDBx/mmJSON format | 6a9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a9s_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 6a9s_full_validation.pdf.gz | 435.8 KB | Display | |
Data in XML | 6a9s_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 6a9s_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/6a9s ftp://data.pdbj.org/pub/pdb/validation_reports/a9/6a9s | HTTPS FTP |
-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
#1: Protein | Mass: 46791.219 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: VACWR149, A26L / Production host: Escherichia coli (E. coli) / References: UniProt: P24758 | ||
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#2: Chemical | ChemComp-EDO / #3: 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: 1.95 Å3/Da / Density % sol: 36.88 % |
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Crystal grow | Temperature: 298 K / Method: evaporation Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris pH 8.5, 30 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.97907 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: May 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→20 Å / Num. obs: 114858 / % possible obs: 99.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.18→1.22 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10993 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.18→20 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.97 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.022 Å2
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Refinement step | Cycle: 1 / Resolution: 1.18→20 Å
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Refine LS restraints |
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