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- PDB-7p0u: ORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p0u | ||||||
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Title | ORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 peptide | ||||||
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![]() | APOPTOSIS / ORF virus / Bcl-2 | ||||||
Function / homology | ![]() positive regulation of release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / positive regulation of apoptotic process / apoptotic process / mitochondrion / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suraweera, C.D. / Hinds, M.G. / Kvansakul, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Investigation of Orf Virus Bcl-2 Homolog ORFV125 Interactions with BH3-Motifs from BH3-Only Proteins Puma and Hrk. Authors: Suraweera, C.D. / Hinds, M.G. / Kvansakul, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 285.2 KB | Display | ![]() |
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PDB format | ![]() | 191.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 495.9 KB | Display | ![]() |
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Full document | ![]() | 504 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 31.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p0sC ![]() 7adtS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16160.256 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2973.417 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.33 % / Description: single thick cuboid like crystal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Bis-Tris propane pH 8.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.99374263399→38.5694114058 Å / Num. obs: 40304 / % possible obs: 95.9 % / Redundancy: 2.7 % / Biso Wilson estimate: 47.6239163241 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.11 |
Reflection shell | Resolution: 1.99374263399→2.05 Å / Rmerge(I) obs: 1.46 / Num. unique obs: 2890 / CC1/2: 0.251 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7ADT Resolution: 1.99374263399→38.5694114058 Å / SU ML: 0.364402590205 / Cross valid method: FREE R-VALUE / σ(F): 1.95836316789 / Phase error: 37.5324817813 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 69.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99374263399→38.5694114058 Å
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Refine LS restraints |
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LS refinement shell |
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