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Yorodumi- PDB-6axs: Structure of the V11I/T58A/P122A mutant of the HIV-1 capsid protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 6axs | ||||||
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Title | Structure of the V11I/T58A/P122A mutant of the HIV-1 capsid protein | ||||||
Components | HIV-1 capsid protein | ||||||
Keywords | VIRAL PROTEIN / HIV-1 capsid protein / hexamer / V11I/T58A/P122A mutant | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity ...viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.402 Å | ||||||
Authors | Gres, A.T. / Kirby, K.A. / Sarafianos, S.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Identification of a novel element in HIV-1 capsid critical for assembly and maturation Authors: Novikova, M. / Gres, A.T. / Kirby, K.A. / Sarafianos, S.G. / Freed, E.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6axs.cif.gz | 103.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6axs.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 6axs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/6axs ftp://data.pdbj.org/pub/pdb/validation_reports/ax/6axs | HTTPS FTP |
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-Related structure data
Related structure data | 6axtC 6axvC 6axxC 6axyC 4xfxS S: Starting model for refinement C: citing same article (ref.) |
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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: 25588.389 Da / Num. of mol.: 1 / Fragment: UNP residues 133-363 / Mutation: V11I, T58A, P122A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6DRA0, UniProt: P12493*PLUS | ||||
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#2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.79 % / Mosaicity: 0.29 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaI, Sodium cacodylate, Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000032 Å | ||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Dec 19, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.000032 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.4→36.076 Å / Num. obs: 10917 / % possible obs: 98.2 % / Redundancy: 10.5 % / Biso Wilson estimate: 48.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.025 / Rrim(I) all: 0.082 / Net I/σ(I): 20.7 / Num. measured all: 114114 / Scaling rejects: 0 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdbid 4XFX Resolution: 2.402→36.076 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.72 Å2 / Biso mean: 61.0166 Å2 / Biso min: 27.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.402→36.076 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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