+Open data
-Basic information
Entry | Database: PDB / ID: 5a8u | ||||||
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Title | Crystal structure of Orgyia pseudotsugata CPV5 polyhedra | ||||||
Components | POLYHEDRIN | ||||||
Keywords | VIRAL PROTEIN / INSECT VIRUS OCCLUSION BODY / MICROCRYSTAL | ||||||
Function / homology | viral occlusion body / Polyhedrin Function and homology information | ||||||
Biological species | ORGYIA PSEUDOTSUGATA CYPOVIRUS 5 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.609 Å | ||||||
Authors | Ji, X. / Axford, D. / Owen, R. / Evans, G. / Ginn, H.M. / Sutton, G. / Stuart, D.I. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2015 Title: Polyhedra Structures and the Evolution of the Insect Viruses. Authors: Ji, X. / Axford, D. / Owen, R. / Evans, G. / Ginn, H.M. / Sutton, G. / Stuart, D.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a8u.cif.gz | 65.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a8u.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 5a8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/5a8u ftp://data.pdbj.org/pub/pdb/validation_reports/a8/5a8u | HTTPS FTP |
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-Related structure data
Related structure data | 5a8sC 5a8tC 5a8vSC 5a96C 5a98C 5a99C 5a9aC 5a9bC 5a9cC 5a9pC C: citing same article (ref.) S: Starting model for refinement |
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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: 28348.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ORGYIA PSEUDOTSUGATA CYPOVIRUS 5 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P36701 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 26 |
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-Sample preparation
Crystal | Density Matthews: 1.6 Å3/Da / Density % sol: 22 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→51.2 Å / Num. obs: 23283 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 14.8 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.34 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.61→1.65 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A8V Resolution: 1.609→51.16 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 18.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.551 Å2 / ksol: 0.431 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.609→51.16 Å
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Refine LS restraints |
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LS refinement shell |
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