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Yorodumi- PDB-4rfu: Crystal structure of truncated P-domain from Grouper nervous necr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rfu | ||||||
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Title | Crystal structure of truncated P-domain from Grouper nervous necrosis virus capsid protein at 1.2A | ||||||
Components | Coat protein | ||||||
Keywords | VIRAL PROTEIN / Protrusion domain | ||||||
Function / homology | Nodavirus capsid / nodavirus capsid protein / Viral coat protein subunit / viral capsid / metal ion binding / DI(HYDROXYETHYL)ETHER / Capsid protein alpha Function and homology information | ||||||
Biological species | Epinephelus coioides nervous necrosis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Chen, N.C. / Chen, C.J. / Yoshimura, M. / Guan, H.H. / Chen, T.Y. | ||||||
Citation | Journal: Plos Pathog. / Year: 2015 Title: Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection Authors: Chen, N.C. / Yoshimura, M. / Guan, H.H. / Wang, T.Y. / Misumi, Y. / Lin, C.C. / Chuankhayan, P. / Nakagawa, A. / Chan, S.I. / Tsukihara, T. / Chen, T.Y. / Chen, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rfu.cif.gz | 95.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rfu.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rfu_validation.pdf.gz | 461.1 KB | Display | wwPDB validaton report |
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Full document | 4rfu_full_validation.pdf.gz | 463 KB | Display | |
Data in XML | 4rfu_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 4rfu_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/4rfu ftp://data.pdbj.org/pub/pdb/validation_reports/rf/4rfu | HTTPS FTP |
-Related structure data
Related structure data | 4rftC 4wizSC C: citing same article (ref.) 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: 13832.235 Da / Num. of mol.: 3 / Fragment: UNP residues 215-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Epinephelus coioides nervous necrosis virus Production host: Escherichia coli (E. coli) / References: UniProt: Q8JNX5 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PEG / | #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: 2.8 Å3/Da / Density % sol: 56.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Ca acetate, 0.1M MES, pH 6.5, 10% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 8, 2014 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. all: 144895 / Num. obs: 144895 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.2→1.21 Å / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WIZ Resolution: 1.2→20.762 Å / SU ML: 0.1 / σ(F): 1.33 / Phase error: 17.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→20.762 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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