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Yorodumi- PDB-2gu0: Crystal Structure of Human Rotavirus NSP2 (Group C / Bristol Strain) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gu0 | ||||||
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Title | Crystal Structure of Human Rotavirus NSP2 (Group C / Bristol Strain) | ||||||
Components | Nonstructural protein 2 | ||||||
Keywords | VIRAL PROTEIN / NSP2 / rotavirus / HIT motif / Bristol | ||||||
Function / homology | Function and homology information hydrolase activity, acting on acid anhydrides / viral genome replication / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Human rotavirus C | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Jiang, X. / Prasad, B.V.V. | ||||||
Citation | Journal: J.Virol. / Year: 2006 Title: Structure-function analysis of rotavirus NSP2 octamer by using a novel complementation system Authors: Taraporewala, Z.F. / Jiang, X. / Vasquez-Del Carpio, R. / Jayaram, H. / Prasad, B.V.V. / Patton, J.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gu0.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gu0.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 2gu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gu0_validation.pdf.gz | 421.1 KB | Display | wwPDB validaton report |
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Full document | 2gu0_full_validation.pdf.gz | 435.6 KB | Display | |
Data in XML | 2gu0_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 2gu0_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/2gu0 ftp://data.pdbj.org/pub/pdb/validation_reports/gu/2gu0 | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | The biological assembly is a octamer generated from the two monomers in the asymmetric unit by the operations: (-x, -y, z), (-y, x, z) and (y, -x, z). |
-Components
#1: Protein | Mass: 35964.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rotavirus C / Species: Rotavirus C / Strain: Bristol / Gene: NSP2, segment 9 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q9PY93 |
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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: 3.51 Å3/Da / Density % sol: 64.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 1.5-1.7M ammonium sulfate, 0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2004 |
Radiation | Monochromator: high-resolution double-crystal sagittal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→500 Å / Num. all: 23492 / Num. obs: 23468 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 5.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 19.957 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.124 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→500 Å
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Refine LS restraints |
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Xplor file |
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