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Yorodumi- PDB-7c21: Crystal structure of Duvenhage virus phosphoprotein C-terminal domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c21 | ||||||
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Title | Crystal structure of Duvenhage virus phosphoprotein C-terminal domain | ||||||
Components | Phosphoprotein | ||||||
Keywords | VIRAL PROTEIN / phosphoprotein | ||||||
Function / homology | Function and homology information virion component => GO:0044423 / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-dependent RNA polymerase activity Similarity search - Function | ||||||
Biological species | Duvenhage virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Sugiyama, A. / Jiang, X. / Maenaka, K. / Yao, M. / Ose, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Structural comparison of the C-terminal domain of functionally divergent lyssavirus P proteins. Authors: Sugiyama, A. / Nomai, T. / Jiang, X. / Minami, M. / Yao, M. / Maenaka, K. / Ito, N. / Gooley, P.R. / Moseley, G.W. / Ose, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c21.cif.gz | 35.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c21.ent.gz | 22.2 KB | Display | PDB format |
PDBx/mmJSON format | 7c21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c21_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
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Full document | 7c21_full_validation.pdf.gz | 430.5 KB | Display | |
Data in XML | 7c21_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 7c21_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/7c21 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/7c21 | HTTPS FTP |
-Related structure data
Related structure data | 7c20C 1vyiS 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: 12870.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Duvenhage virus / Production host: Escherichia coli (E. coli) / References: UniProt: D2CRL7 |
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#2: 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: 2.42 Å3/Da / Density % sol: 49.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH7.5, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→43.8 Å / Num. obs: 8380 / % possible obs: 98 % / Redundancy: 8.6 % / Biso Wilson estimate: 23.57 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.216 / Net I/σ(I): 7.53 |
Reflection shell | Resolution: 1.95→2.07 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 1.56 / Num. unique obs: 1361 / CC1/2: 0.607 / Rrim(I) all: 1.385 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VYI Resolution: 1.95→43.8 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→43.8 Å
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Refine LS restraints |
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LS refinement shell |
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