+Open data
-Basic information
Entry | Database: PDB / ID: 5a96 | ||||||
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Title | Crystal structure of Lymantria dispar CPV14 polyhedra | ||||||
Components | POLYHEDRIN | ||||||
Keywords | VIRAL PROTEIN / INSECT VIRUS OCCLUSION BODY / MICROCRYSTAL | ||||||
Function / homology | Cypovirus polyhedrin / Cypovirus polyhedrin / GTP binding / GUANOSINE-5'-TRIPHOSPHATE / Polyhedrin Function and homology information | ||||||
Biological species | LYMANTRIA DISPAR CYPOVIRUS 14 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.914 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 | 5a96.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a96.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 5a96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a96_validation.pdf.gz | 859.8 KB | Display | wwPDB validaton report |
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Full document | 5a96_full_validation.pdf.gz | 861.3 KB | Display | |
Data in XML | 5a96_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 5a96_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/5a96 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/5a96 | HTTPS FTP |
-Related structure data
Related structure data | 5a8sC 5a8tC 5a8uC 5a8vC 5a98C 5a99C 5a9aC 5a9bC 5a9cC 5a9pC 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: 28723.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DISULFIDE BOND BETWEEN A 68 AND A 97 / Source: (gene. exp.) LYMANTRIA DISPAR CYPOVIRUS 14 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q91IE3 |
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#2: Chemical | ChemComp-GTP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 20 |
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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: DECTRIS PILATUS / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→72.5 Å / Num. obs: 12952 / % possible obs: 92.3 % / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Biso Wilson estimate: 10.86 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.91→2.02 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.8 / % possible all: 52.1 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 1.914→32.445 Å / SU ML: 0.15 / σ(F): 1.36 / Phase error: 18.19 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.426 Å2 / ksol: 0.462 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.914→32.445 Å
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Refine LS restraints |
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LS refinement shell |
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