+Open data
-Basic information
Entry | Database: PDB / ID: 3rkc | ||||||
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Title | Hepatitis E Virus Capsid Protein E2s Domain (genotype IV) | ||||||
Components | Capsid protein | ||||||
Keywords | VIRAL PROTEIN / Viral Capsid Protein | ||||||
Function / homology | : / : / Structural protein 2 second domain / Structural protein 2 C-terminal domain / structural molecule activity / RNA binding / identical protein binding / Capsid protein Function and homology information | ||||||
Biological species | Hepatitis E virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Tang, X.H. / Sivaraman, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structural basis for the neutralization and genotype specificity of hepatitis E virus Authors: Tang, X.H. / Yang, C.Y. / Gu, Y. / Song, C.L. / Zhang, X. / Wang, Y.B. / Zhang, J. / Hew, C.L. / Li, S.W. / Xia, N.S. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rkc.cif.gz | 80.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rkc.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 3rkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rkc_validation.pdf.gz | 431 KB | Display | wwPDB validaton report |
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Full document | 3rkc_full_validation.pdf.gz | 432.5 KB | Display | |
Data in XML | 3rkc_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 3rkc_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/3rkc ftp://data.pdbj.org/pub/pdb/validation_reports/rk/3rkc | HTTPS FTP |
-Related structure data
Related structure data | 3rkdC 3ggqS 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: 15988.812 Da / Num. of mol.: 2 / Fragment: UNP residues 93-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis E virus / Plasmid: pTO-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: D3VV84 #2: 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: 2.21 Å3/Da / Density % sol: 44.29 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris, 20% PEG 10000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Nov 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. all: 26223 / Num. obs: 26223 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GGQ Resolution: 1.79→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 49.6549 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.3327 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→20 Å
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Refine LS restraints |
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