+Open data
-Basic information
Entry | Database: PDB / ID: 5a99 | ||||||
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Title | Crystal structure of Operophtera brumata CPV19 polyhedra | ||||||
Components | POLYHEDRIN | ||||||
Keywords | VIRAL PROTEIN / INSECT VIRUS OCCLUSION BODY / MICROCRYSTAL | ||||||
Function / homology | ATP binding / metal ion binding / ADENOSINE-5'-TRIPHOSPHATE / Polyhedrin Function and homology information | ||||||
Biological species | OPEROPHTERA BRUMATA CYPOVIRUS 19 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.511 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 | 5a99.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a99.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 5a99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a99_validation.pdf.gz | 784.9 KB | Display | wwPDB validaton report |
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Full document | 5a99_full_validation.pdf.gz | 785 KB | Display | |
Data in XML | 5a99_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 5a99_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/5a99 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/5a99 | HTTPS FTP |
-Related structure data
Related structure data | 5a8sC 5a8tC 5a8uC 5a8vC 5a96C 5a98C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29117.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) OPEROPHTERA BRUMATA CYPOVIRUS 19 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q30C66 |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 34 |
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-Sample preparation
Crystal | Density Matthews: 1.6 Å3/Da / Density % sol: 21 % / 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: 1.5→51.4 Å / Num. obs: 21653 / % possible obs: 75.5 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.37 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 0.3 / % possible all: 12.2 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 1.511→41.935 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 23.62 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.701 Å2 / ksol: 0.515 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.511→41.935 Å
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Refine LS restraints |
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LS refinement shell |
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