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Yorodumi- PDB-4v86: Structure-function Analysis of Receptor-binding in Adeno-Associat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v86 | |||||||||
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Title | Structure-function Analysis of Receptor-binding in Adeno-Associated Virus Serotype 6 (AAV-6) | |||||||||
Components | Capsid protein VP1 | |||||||||
Keywords | VIRUS / beta barrel | |||||||||
Function / homology | Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein VP1 Function and homology information | |||||||||
Biological species | Adeno-associated virus - 6 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.003 Å | |||||||||
Authors | Xie, Q. | |||||||||
Citation | Journal: Virology / Year: 2011 Title: Structure-function analysis of receptor-binding in adeno-associated virus serotype 6 (AAV-6). Authors: Xie, Q. / Lerch, T.F. / Meyer, N.L. / Chapman, M.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v86.cif.gz | 5.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v86.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v86 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v86 | HTTPS FTP |
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-Related 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: 58360.598 Da / Num. of mol.: 60 / Fragment: UNP residues 217-736 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Adeno-associated virus - 6 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: O56137 |
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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: 3.43 Å3/Da / Density % sol: 64.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 4-6% PEG6000, 100 mM HEPES, 50 mM magnesium chloride,, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 1, 2004 |
Radiation | Monochromator: Single-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9186 Å / Relative weight: 1 |
Reflection | Resolution: 3.003→49.21 Å / Num. all: 332221 / Num. obs: 332221 / % possible obs: 42 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 3.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.003→49.21 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.96 / σ(F): 0 / Phase error: 31.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.443 Å2 / ksol: 0.328 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.19 Å2 / Biso mean: 62.7664 Å2 / Biso min: 35.63 Å2
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Refinement step | Cycle: LAST / Resolution: 3.003→49.21 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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