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Yorodumi- PDB-5na2: Crystal structure of the full-length Feline Immunodeficiency Viru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5na2 | ||||||
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Title | Crystal structure of the full-length Feline Immunodeficiency Virus capsid protein unveils original features | ||||||
Components | Capsid protein (p24) | ||||||
Keywords | VIRAL PROTEIN / FIV / Capsid / p24 / CA / Feline Immunodeficiency Virus | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / viral nucleocapsid / nucleic acid binding / structural constituent of virion / zinc ion binding Similarity search - Function | ||||||
Biological species | Feline immunodeficiency virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Folio, C. / Sierra, N. / Dujardin, M. / Alvarez, G. / Guillon, C. | ||||||
Citation | Journal: Viruses / Year: 2017 Title: Crystal Structure of the Full-Length Feline Immunodeficiency Virus Capsid Protein Shows an N-Terminal beta-Hairpin in the Absence of N-Terminal Proline. Authors: Folio, C. / Sierra, N. / Dujardin, M. / Alvarez, G. / Guillon, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5na2.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5na2.ent.gz | 85.5 KB | Display | PDB format |
PDBx/mmJSON format | 5na2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5na2_validation.pdf.gz | 448.6 KB | Display | wwPDB validaton report |
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Full document | 5na2_full_validation.pdf.gz | 453.5 KB | Display | |
Data in XML | 5na2_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 5na2_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/5na2 ftp://data.pdbj.org/pub/pdb/validation_reports/na/5na2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23636.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Feline immunodeficiency virus (isolate Petaluma) Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P16087 #2: Chemical | ChemComp-GOL / #3: 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: 2.85 Å3/Da / Density % sol: 56.92 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 0.2 M magnesium sulfate, 20% PEG 4000, 10% glycerol, 10% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.99187 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→59.719 Å / Num. obs: 39411 / % possible obs: 91.2 % / Redundancy: 2.38 % / Rsym value: 0.0354 / Net I/σ(I): 16.42 |
Reflection shell | Resolution: 1.9→2.01 Å / Mean I/σ(I) obs: 3.33 / Rrim(I) all: 0.0325 / Rsym value: 0.0258 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XGU (N-terminal domain) and 5DCK (C-terminal domain) Resolution: 1.67→38.499 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.71 / 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: 1.67→38.499 Å
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Refine LS restraints |
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LS refinement shell |
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