+Open data
-Basic information
Entry | Database: PDB / ID: 5vmn | ||||||
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Title | Crystal structure of grouper iridovirus GIV66 | ||||||
Components | Bak protein | ||||||
Keywords | VIRAL PROTEIN / Apoptosis / Bcl-2 / iridovirus / grouper | ||||||
Function / homology | : / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / membrane / NITRATE ION / Bak protein Function and homology information | ||||||
Biological species | Grouper iridovirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Banjara, S. / Kvansakul, M. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Grouper iridovirus GIV66 is a Bcl-2 protein that inhibits apoptosis by exclusively sequestering Bim. Authors: Banjara, S. / Mao, J. / Ryan, T.M. / Caria, S. / Kvansakul, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vmn.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vmn.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 5vmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/5vmn ftp://data.pdbj.org/pub/pdb/validation_reports/vm/5vmn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14943.972 Da / Num. of mol.: 1 / Fragment: UNP residues 1-127 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Grouper iridovirus / Gene: GIV66 / Plasmid: pGEX-6P3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5GAF0 | ||||
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#2: Chemical | ChemComp-NO3 / #3: Chemical | ChemComp-EDO / #4: 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: 3.32 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 4.0 M sodium nitrate with 0.1 M sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→42.91 Å / Num. obs: 24871 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 11.1 % / Rmerge(I) obs: 2.395 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1219 / CC1/2: 0.396 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→41.964 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.6 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→41.964 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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