+Open data
-Basic information
Entry | Database: PDB / ID: 7rlm | |||||||||
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Title | Crystal Structure of Potato Leafroll Virus (PLRV) Coat Protein | |||||||||
Components | Coat protein | |||||||||
Keywords | VIRAL PROTEIN / PLRV / polerovirus / icosahedral virus / quasi-equivalence / viral assembly / capsid / plant virus | |||||||||
Function / homology | Luteovirus group 1 coat protein / Luteovirus coat protein / Viral coat protein subunit / viral capsid / structural molecule activity / BROMIDE ION / Coat protein Function and homology information | |||||||||
Biological species | Potato leafroll virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Adams, M.C. / Chappie, J.S. / Schiltz, C.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Struct.Biol. / Year: 2021 Title: Crystal structure of the potato leafroll virus coat protein and implications for viral assembly. Authors: Adams, M.C. / Schiltz, C.J. / Heck, M.L. / Chappie, J.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rlm.cif.gz | 204.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rlm.ent.gz | 148.6 KB | Display | PDB format |
PDBx/mmJSON format | 7rlm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rlm_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 7rlm_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 7rlm_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 7rlm_validation.cif.gz | 55.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/7rlm ftp://data.pdbj.org/pub/pdb/validation_reports/rl/7rlm | HTTPS FTP |
-Related structure data
Related structure data | 6scoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 15569.415 Da / Num. of mol.: 6 / Fragment: UNP residues 68-208 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Potato leafroll virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76QV9 #2: Chemical | ChemComp-BR / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.93 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris propane, pH 7.7, 26% PEG3350, 0.1 M sodium bromide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.504→72.86 Å / Num. obs: 177750 / % possible obs: 89.13 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.79 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.504→1.558 Å / Num. unique obs: 6323 / CC1/2: 0.315 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6SCO Resolution: 1.8→72.86 Å / SU ML: 0.2036 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 22.5047 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→72.86 Å
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Refine LS restraints |
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LS refinement shell |
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