+Open data
-Basic information
Entry | Database: PDB / ID: 6erm | ||||||
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Title | HIV Hexamer with 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: 2 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 | 6erm.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6erm.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 6erm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6erm_validation.pdf.gz | 686.6 KB | Display | wwPDB validaton report |
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Full document | 6erm_full_validation.pdf.gz | 688.7 KB | Display | |
Data in XML | 6erm_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 6erm_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/6erm ftp://data.pdbj.org/pub/pdb/validation_reports/er/6erm | HTTPS FTP |
-Related structure data
Related structure data | 6ernC 6r6qC 6r8cC 5hgmS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24504.178 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: B6DRA0 |
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#2: Chemical | ChemComp-AZT / |
#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: 2.98 Å3/Da / Density % sol: 58.76 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / Details: PEG4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å |
Detector | Type: OXFORD RUBY CCD / Detector: CCD / Date: Jan 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→78 Å / Num. obs: 18217 / % possible obs: 100 % / Redundancy: 9.3 % / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2→2.03 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HGM Resolution: 2→78 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.466 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.154 / 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: 29.017 Å2
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Refinement step | Cycle: 1 / Resolution: 2→78 Å
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Refine LS restraints |
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