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Yorodumi- PDB-6xy4: Structural insight into sheep-pox virus mediated inhibition of ap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xy4 | |||||||||
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Title | Structural insight into sheep-pox virus mediated inhibition of apoptosis | |||||||||
Components |
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Keywords | APOPTOSIS / Pox virus / Bcl-2 | |||||||||
Function / homology | Function and homology information : / 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 Similarity search - Function | |||||||||
Biological species | Sheeppox virus Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04623155256 Å | |||||||||
Authors | Suraweera, C.D. / Hinds, M.G. / Kvansakul, M. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Febs Lett. / Year: 2020 Title: Crystal structures of the sheeppox virus encoded inhibitor of apoptosis SPPV14 bound to the proapoptotic BH3 peptides Hrk and Bax. Authors: Suraweera, C.D. / Burton, D.R. / Hinds, M.G. / Kvansakul, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xy4.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xy4.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 6xy4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xy4_validation.pdf.gz | 426.1 KB | Display | wwPDB validaton report |
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Full document | 6xy4_full_validation.pdf.gz | 427.6 KB | Display | |
Data in XML | 6xy4_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 6xy4_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/6xy4 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/6xy4 | HTTPS FTP |
-Related structure data
Related structure data | 6xy6C 2bjyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17476.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sheeppox virus (strain Turkey/TU-V02127) Gene: SPPV_14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A3F2YKH3 |
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#2: Protein/peptide | Mass: 2973.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O00198 |
#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: 2.2 Å3/Da / Density % sol: 44.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Bis-Tris propane pH 6.5, 20% w/vPEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.046→31.07 Å / Num. obs: 11236 / % possible obs: 98.2 % / Redundancy: 5 % / Biso Wilson estimate: 39.8950367928 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.05→8.92 Å / Num. unique obs: 782 / CC1/2: 0.573 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BJY Resolution: 2.04623155256→31.0657632133 Å / SU ML: 0.237702211781 / Cross valid method: FREE R-VALUE / σ(F): 1.38553218358 / Phase error: 26.211733487 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: 64.7478958779 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04623155256→31.0657632133 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -18.4590111381 Å / Origin y: -12.5771924003 Å / Origin z: -11.1701382726 Å
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Refinement TLS group | Selection details: all |