+Open data
-Basic information
Entry | Database: PDB / ID: 6s5i | ||||||
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Title | Structure of the Lausanne variant of myxoma virus M062 protein | ||||||
Components | M62R | ||||||
Keywords | VIRAL PROTEIN / myxoma virus / M062 / SAMD9 / C7L superfamily / host-range factor / innate immunity / viral antagonism | ||||||
Function / homology | Poxvirus C7/F8A / Poxvirus C7/F8A protein / viral process / NICKEL (II) ION / M062R Function and homology information | ||||||
Biological species | Myxoma virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | O'Byrne, P. / Khan, A.R. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: To Be Published Title: Structure of the Lausanne variant of myxoma virus M062 protein Authors: O'Byrne, P. / Khan, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s5i.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s5i.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 6s5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s5i_validation.pdf.gz | 399.8 KB | Display | wwPDB validaton report |
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Full document | 6s5i_full_validation.pdf.gz | 401.1 KB | Display | |
Data in XML | 6s5i_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 6s5i_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/6s5i ftp://data.pdbj.org/pub/pdb/validation_reports/s5/6s5i | HTTPS FTP |
-Related structure data
Related structure data | 3cz3S S: Starting model for refinement |
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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: 18650.213 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxoma virus / Gene: m062R, m062R, MYXV_gp066 Production host: Escherichia coli str. 'clone D i2' (bacteria) References: UniProt: B2CWG9 |
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#2: Chemical | ChemComp-NI / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 7.5 50 mM CaCl2 6 - 8% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→47.41 Å / Num. obs: 8422 / % possible obs: 99.55 % / Redundancy: 9.8 % / Biso Wilson estimate: 84.55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05385 / Rpim(I) all: 0.01841 / Rrim(I) all: 0.057 / Net I/σ(I): 23.92 |
Reflection shell | Resolution: 2.45→2.538 Å / Num. unique obs: 846 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3cz3 Resolution: 2.45→47.41 Å / SU ML: 0.3519 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 36.275
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→47.41 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Origin x: 8.51005377608 Å / Origin y: 34.1144657168 Å / Origin z: 34.3344084394 Å
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Refinement TLS group | Selection details: all |