+Open data
-Basic information
Entry | Database: PDB / ID: 4ots | ||||||
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Title | Crystal Structure of isolated Operophtera brumata CPV18 | ||||||
Components | Polyhedrin | ||||||
Keywords | VIRAL PROTEIN / microcrystals / polyhedra / occlusion body | ||||||
Function / homology | Cypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / GTP binding / ATP binding / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Polyhedrin Function and homology information | ||||||
Biological species | Operophtera brumata cypovirus 18 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.704 Å | ||||||
Authors | Stuart, D.I. / Sutton, G.C. / Axford, D. / Ji, X. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: In cellulo structure determination of a novel cypovirus polyhedrin. Authors: Axford, D. / Ji, X. / Stuart, D.I. / Sutton, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ots.cif.gz | 147 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ots.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ots.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/4ots ftp://data.pdbj.org/pub/pdb/validation_reports/ot/4ots | 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28301.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Operophtera brumata cypovirus 18 / Plasmid: pOPIN / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q30C70 |
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-Non-polymers , 5 types, 245 molecules
#2: Chemical | ChemComp-CL / |
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#3: Chemical | ChemComp-GTP / |
#4: Chemical | ChemComp-ATP / |
#5: Chemical | ChemComp-MG / |
#6: 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: 23.08 % |
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Crystal grow | Temperature: 301 K / pH: 7.5 Details: Crystals formed naturally within the cytoplasm and were purified from cells, pH 7.5, temperature 301K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2011 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→72.686 Å / Num. all: 19343 / Num. obs: 19343 / % possible obs: 97.2 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 1.34 |
Reflection shell | Highest resolution: 1.7 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.704→27.473 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 11.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.704→27.473 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -20.9564 Å / Origin y: 8.6787 Å / Origin z: -34.0137 Å
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Refinement TLS group | Selection details: all |