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Yorodumi- PDB-2x82: Evolutionary basis of HIV restriction by the antiretroviral TRIMCyp -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x82 | ||||||
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Title | Evolutionary basis of HIV restriction by the antiretroviral TRIMCyp | ||||||
Components | CAPSID PROTEIN P24 | ||||||
Keywords | VIRAL PROTEIN / TRIM / RESTRICTION FACTOR IMMUNITY | ||||||
Function / homology | Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Orthogonal Bundle / Mainly Alpha Function and homology information | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.6 Å | ||||||
Authors | Price, A.J. / James, L.C. | ||||||
Citation | Journal: Plos Pathog. / Year: 2010 Title: Conformational Adaptation of Asian Macaque Trimcyp Directs Lineage Specific Antiviral Activity. Authors: Ylinen, L.M. / Price, A.J. / Rasaiyaah, J. / Hue, S. / Rose, N.J. / Marzetta, F. / James, L.C. / Towers, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x82.cif.gz | 247.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x82.ent.gz | 205.2 KB | Display | PDB format |
PDBx/mmJSON format | 2x82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/2x82 ftp://data.pdbj.org/pub/pdb/validation_reports/x8/2x82 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16287.562 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 136-280 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE D194) Production host: ESCHERICHIA COLI (E. coli) #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 50 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 22894 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.6 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER / Resolution: 2.6→86.68 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.859 / SU B: 32.425 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R: 1.586 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.087 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→86.68 Å
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