+Open data
-Basic information
Entry | Database: PDB / ID: 5exz | ||||||
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Title | Crystal structure of purified recombinant CPV1 Polyhedra | ||||||
Components | Polyhedrin | ||||||
Keywords | VIRAL PROTEIN / in vivo crystal / polyhedrin | ||||||
Function / homology | Cypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / viral occlusion body / host cell cytoplasm / ADENOSINE-5'-TRIPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Polyhedrin Function and homology information | ||||||
Biological species | Bombyx mori cypovirus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Boudes, M. / Garriga, D. / Coulibaly, F. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: A pipeline for structure determination of in vivo-grown crystals using in cellulo diffraction. Authors: Boudes, M. / Garriga, D. / Fryga, A. / Caradoc-Davies, T. / Coulibaly, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5exz.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5exz.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 5exz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5exz_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5exz_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5exz_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 5exz_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/5exz ftp://data.pdbj.org/pub/pdb/validation_reports/ex/5exz | HTTPS FTP |
-Related structure data
Related structure data | 5exyC 2oh5S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28387.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori cypovirus 1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11041 |
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-Non-polymers , 6 types, 180 molecules
#2: Chemical | ChemComp-CL / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-ATP / | #5: Chemical | ChemComp-CTP / | #6: Chemical | ChemComp-GTP / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.61 Å3/Da / Density % sol: 23.69 % |
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Crystal grow | Temperature: 300 K / Method: in cell Details: The crystals used to determine this structure were directly purified from cells, in vivo crystallization in the cytoplasm of the cell |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: beam collimated to 10 microns | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→30 Å / Num. obs: 13734 / % possible obs: 94.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 5.01 Å2 / Rmerge(I) obs: 0.268 / Rpim(I) all: 0.165 / Rrim(I) all: 0.322 / Χ2: 1.031 / Net I/av σ(I): 4.81 / Net I/σ(I): 4.5 / Num. measured all: 42463 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OH5 Resolution: 1.9→27.57 Å / Cor.coef. Fo:Fc: 0.9423 / Cor.coef. Fo:Fc free: 0.8957 / SU R Cruickshank DPI: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.216 / SU Rfree Blow DPI: 0.162 / SU Rfree Cruickshank DPI: 0.16
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Displacement parameters | Biso max: 63.05 Å2 / Biso mean: 7.6 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→27.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.05 Å / Total num. of bins used: 7
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