+Open data
-Basic information
Entry | Database: PDB / ID: 6r8c | ||||||
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Title | HIV capsid hexamer with IP5 ligand | ||||||
Components | Gag polyprotein | ||||||
Keywords | VIRAL PROTEIN / HIV | ||||||
Function / homology | Function and homology information viral process / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | James, L.C. | ||||||
Citation | Journal: to be published Title: HIV hexamer Authors: James, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r8c.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r8c.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 6r8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r8c_validation.pdf.gz | 1014.8 KB | Display | wwPDB validaton report |
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Full document | 6r8c_full_validation.pdf.gz | 1016 KB | Display | |
Data in XML | 6r8c_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 6r8c_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/6r8c ftp://data.pdbj.org/pub/pdb/validation_reports/r8/6r8c | HTTPS FTP |
-Related structure data
Related structure data | 6ermC 6ernC 6r6qC 6es8S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 22973.498 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: myo-IP5 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: B6DRA0 |
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#2: Chemical | ChemComp-5MY / |
#3: 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: 2.94 Å3/Da / Density % sol: 58.21 % |
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Crystal grow | Temperature: 270 K / Method: batch mode / Details: PEG 6K, 1M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978 Å |
Detector | Type: OXFORD SAPPHIRE CCD / Detector: CCD / Date: Mar 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.913→78.52 Å / Num. obs: 20758 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.93→1.98 Å / Redundancy: 6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1240 / CC1/2: 0.883 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ES8 Resolution: 1.92→29.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.317 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.456 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→29.69 Å
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Refine LS restraints |
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