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Yorodumi- PDB-2vty: Vaccinia virus anti-apoptotic F1L is a novel Bcl-2-like domain sw... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vty | ||||||
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Title | Vaccinia virus anti-apoptotic F1L is a novel Bcl-2-like domain swapped dimer | ||||||
Components | PROTEIN F1 | ||||||
Keywords | APOPTOSIS / BCL-2 / VACCINIA VIRUS | ||||||
Function / homology | Function and homology information : / host cell mitochondrial outer membrane / : / regulation of apoptotic process / membrane Similarity search - Function | ||||||
Biological species | VACCINIA VIRUS | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 2.1 Å | ||||||
Authors | Kvansakul, M. / Yang, H. / Fairlie, W.D. / Czabotar, P.E. / Fischer, S.F. / Perugini, M.A. / Huang, D.C.S. / Colman, P.M. | ||||||
Citation | Journal: Cell Death Differ. / Year: 2008 Title: Vaccinia Virus Anti-Apoptotic F1L is a Novel Bcl-2-Like Domain-Swapped Dimer that Binds a Highly Selective Subset of Bh3-Containing Death Ligands. Authors: Kvansakul, M. / Yang, H. / Fairlie, W.D. / Czabotar, P.E. / Fischer, S.F. / Perugini, M.A. / Huang, D.C.S. / Colman, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vty.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vty.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/2vty ftp://data.pdbj.org/pub/pdb/validation_reports/vt/2vty | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 21456.246 Da / Num. of mol.: 1 / Fragment: RESIDUES 18-186 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VACCINIA VIRUS / Strain: MODIFIED VACCINIA ANKARA / Plasmid: PET DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: O57173 |
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#2: Water | ChemComp-HOH / |
Sequence details | N-TERMINAL HEXAHISTID |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 5.2 / Details: 0.9 NACL, 50 MM NA/K PHOSPHATE PH 5.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 10, 2006 / Details: CAPILLARY OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 13687 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 2.1→88.39 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.556 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.971 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→88.39 Å
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