+Open data
-Basic information
Entry | Database: PDB / ID: 5a9a | ||||||
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Title | Crystal structure of Simulium ubiquitum CPV20 polyhedra | ||||||
Components | POLYHEDRIN | ||||||
Keywords | VIRAL PROTEIN / INSECT VIRUS OCCLUSION BODY / MICROCRYSTAL | ||||||
Function / homology | Cypovirus polyhedrin / Cypovirus polyhedrin / URIDINE 5'-TRIPHOSPHATE / Polyhedrin Function and homology information | ||||||
Biological species | SIMULIUM UBIQUITUM CYPOVIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.822 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 | 5a9a.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a9a.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 5a9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/5a9a ftp://data.pdbj.org/pub/pdb/validation_reports/a9/5a9a | HTTPS FTP |
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-Related structure data
Related structure data | 5a8sC 5a8tC 5a8uC 5a8vC 5a96C 5a98C 5a99C 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: 28195.736 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SIMULIUM UBIQUITUM CYPOVIRUS / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q0MX25 |
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#2: Chemical | ChemComp-UTP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 51 |
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-Sample preparation
Crystal | Density Matthews: 1.6 Å3/Da / Density % sol: 24.6 % / 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 6M / 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: 1.82→51.7 Å / Num. obs: 16582 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 10 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.34 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.82→1.87 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.1 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MODELS OF POLYHEDRA STRUCTURE OF CPV5, CPV4, CPV1, CPV14, CPV15 AND CPV19 Resolution: 1.822→42.197 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 17.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.791 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.822→42.197 Å
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Refine LS restraints |
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LS refinement shell |
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