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Yorodumi- PDB-5y9r: Crystal structure of the oligomerization domain of NSP4 from rota... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y9r | ||||||
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Title | Crystal structure of the oligomerization domain of NSP4 from rotavirus strain MF66 | ||||||
Components | Nonstructural protein 4 | ||||||
Keywords | VIRAL PROTEIN / antiparallel / tetramer / coiled-coil / nickel bound | ||||||
Function / homology | Function and homology information host caveola / host cell rough endoplasmic reticulum membrane / protein complex oligomerization / monoatomic ion channel activity / toxin activity / induction by virus of host autophagy / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Bovine rotavirus G10 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Suguna, K. / Kumar, S. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: New tetrameric forms of the rotavirus NSP4 with antiparallel helices Authors: Suguna, K. / Kumar, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y9r.cif.gz | 47.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y9r.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 5y9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y9r_validation.pdf.gz | 458.4 KB | Display | wwPDB validaton report |
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Full document | 5y9r_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 5y9r_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 5y9r_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/5y9r ftp://data.pdbj.org/pub/pdb/validation_reports/y9/5y9r | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5649.737 Da / Num. of mol.: 4 / Fragment: UNP residues 95-139 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bovine rotavirus G10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6QT01 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CD / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.5 % |
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Crystal grow | Temperature: 299 K / Method: microbatch / pH: 4.5 Details: 0.1M sodium acetate trihydrate, 24% PEG 2000, 10mM magnesium chloride, 10mM nickel chloride, 10mM cadmium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 29, 2015 / Details: bent collimating mirror and toroid |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→62.6 Å / Num. obs: 9675 / % possible obs: 98.8 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.047 / Rrim(I) all: 0.079 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 821 / CC1/2: 0.875 / Rpim(I) all: 0.31 / Rrim(I) all: 0.52 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.595 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→39.595 Å
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Refine LS restraints |
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LS refinement shell |
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