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Yorodumi- PDB-8qqc: Crystal structure of Lymantria dispar CPV14 polyhedra single crystal -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qqc | ||||||
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Title | Crystal structure of Lymantria dispar CPV14 polyhedra single crystal | ||||||
Components | Polyhedrin | ||||||
Keywords | VIRAL PROTEIN / Polyhedrin / GTP binding | ||||||
Function / homology | Cypovirus polyhedrin / Cypovirus polyhedrin / GTP binding / GUANOSINE-5'-TRIPHOSPHATE / Polyhedrin Function and homology information | ||||||
Biological species | Lymantria dispar (gypsy moth) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Trincao, J. / Warren, A. / Crawshaw, A. / Sutton, G. / Stuart, D. / Evans, G. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: VMXm - sub-micron microfocus beamline for macromolecular crystallography at Diamond Light Source Authors: Warren, A.J. / Trincao, J. / Crawshaw, A.D. / Beale, E. / Duller, G. / Stallwood, A. / Lunnon, M. / Littlewood, R. / Prescott, A. / Foster, A. / Smith, N. / Rehm, G. / Gayadeen, S. / ...Authors: Warren, A.J. / Trincao, J. / Crawshaw, A.D. / Beale, E. / Duller, G. / Stallwood, A. / Lunnon, M. / Littlewood, R. / Prescott, A. / Foster, A. / Smith, N. / Rehm, G. / Gayadeen, S. / Bloomer, C. / Alianelli, L. / Laundy, D. / Sutter, J. / Cahill, L. / Evans, G. #1: 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 | 8qqc.cif.gz | 133.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qqc.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 8qqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/8qqc ftp://data.pdbj.org/pub/pdb/validation_reports/qq/8qqc | HTTPS FTP |
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-Related structure data
Related structure data | 8qphC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 28723.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lymantria dispar (gypsy moth) / Gene: pod / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q91IE3 |
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#2: Chemical | ChemComp-GTP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.6 Å3/Da / Density % sol: 22 % / Description: Cubic |
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Crystal grow | Temperature: 300 K / Method: in cell / pH: 7.5 / Details: In vivo |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: VMXm / Wavelength: 0.5814 Å |
Detector | Type: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Sep 29, 2021 |
Radiation | Monochromator: Horizontal Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.5814 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→42.1 Å / Num. obs: 40615 / % possible obs: 90.69 % / Redundancy: 4.5 % / CC1/2: 0.911 / Rmerge(I) obs: 0.304 / Rpim(I) all: 0.146 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 2.02 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1275 / CC1/2: 0.356 / Rpim(I) all: 0.696 / % possible all: 57.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→36.45 Å / SU ML: 0.2098 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3356 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→36.45 Å
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Refine LS restraints |
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LS refinement shell |
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