+Open data
-Basic information
Entry | Database: PDB / ID: 1ny7 | ||||||
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Title | COWPEA MOSAIC VIRUS (CPMV) | ||||||
Components |
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Keywords | VIRUS / COMOVIRUS / VIRAL COAT PROTEIN / COWPEA MOSAIC VIRUS (CPMV) / Icosahedral virus | ||||||
Function / homology | Function and homology information transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / host cell nucleus / GTP binding / structural molecule activity / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | Cowpea mosaic virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR, molecular replacement / Resolution: 3 Å | ||||||
Authors | Lin, T. / Chen, Z. / Usha, R. / Stauffacher, C.V. / Dai, J.-B. / Schmidt, T. / Johnson, J.E. | ||||||
Citation | Journal: Virology / Year: 1999 Title: The Refined Crystal Structure of Cowpea Mosaic Virus at 2.8A Resolution Authors: Lin, T. / Chen, Z. / Usha, R. / Stauffacher, C.V. / Dai, J.-B. / Schmidt, T. / Johnson, J.E. #1: Journal: Crystallography in Molecular Biology / Year: 1987 Title: The structure of cowpea mosaic virus at 3.5 A resolution Authors: Stauffacher, C.V. / Usha, R. / Harrington, M. / Schmidt, T. / Hosur, M. / Johnson, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ny7.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ny7.ent.gz | 95.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ny7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ny7_validation.pdf.gz | 423.3 KB | Display | wwPDB validaton report |
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Full document | 1ny7_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 1ny7_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 1ny7_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/1ny7 ftp://data.pdbj.org/pub/pdb/validation_reports/ny/1ny7 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 20961.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cowpea mosaic virus / Genus: Comovirus / References: UniProt: P03599 |
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#2: Protein | Mass: 40858.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cowpea mosaic virus / Genus: Comovirus / References: UniProt: P03599 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, potasium phosphate, ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.5 Å |
Detector | Type: KODAK / Detector: FILM / Details: mirror |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. all: 105051 / Num. obs: 89846 / % possible obs: 85.53 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 14.8 Å2 |
Reflection shell | Resolution: 3→3.18 Å / % possible all: 71.5 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 102333 / Num. measured all: 285379 / Rmerge(I) obs: 0.109 |
-Processing
Software |
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Refinement | Method to determine structure: SIR, molecular replacement / Resolution: 3→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 14.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.18 Å / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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