+Open data
-Basic information
Entry | Database: PDB / ID: 4htw | ||||||
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Title | SIVmac239 capsid N-terminal domain | ||||||
Components | Gag protein | ||||||
Keywords | VIRAL PROTEIN / SIV capsid protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Simian immunodeficiency virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å | ||||||
Authors | Schmidt, A.G. | ||||||
Citation | Journal: Plos Pathog. / Year: 2013 Title: Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5alpha Specificity. Authors: McCarthy, K.R. / Schmidt, A.G. / Kirmaier, A. / Wyand, A.L. / Newman, R.M. / Johnson, W.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4htw.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4htw.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 4htw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4htw_validation.pdf.gz | 416.3 KB | Display | wwPDB validaton report |
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Full document | 4htw_full_validation.pdf.gz | 421.3 KB | Display | |
Data in XML | 4htw_validation.xml.gz | 8 KB | Display | |
Data in CIF | 4htw_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/4htw ftp://data.pdbj.org/pub/pdb/validation_reports/ht/4htw | 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 | Mass: 16198.291 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 3-145 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian immunodeficiency virus / Gene: synthetic / Plasmid: pET303 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Q5M0 |
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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: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 10% PEG 2000 MME, 10mM nickel chloride and 100mM Tris., pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 3537 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.063 / Χ2: 3.954 / Net I/σ(I): 10.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.273 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.12 / σ(F): 1.36 / Phase error: 38.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.574 Å2 / ksol: 0.298 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 205.94 Å2 / Biso mean: 109.2306 Å2 / Biso min: 68.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→29.273 Å
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