+Open data
-Basic information
Entry | Database: PDB / ID: 1lg7 | ||||||
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Title | Crystal structure of Vesicular Stomatitis Virus Matrix Protein | ||||||
Components | VSV matrix protein | ||||||
Keywords | VIRAL PROTEIN / VIRUS MATRIX | ||||||
Function / homology | Function and homology information host cell nuclear membrane / viral budding via host ESCRT complex / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host gene expression / structural constituent of virion / viral envelope / virion membrane Similarity search - Function | ||||||
Biological species | Vesicular stomatitis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.96 Å | ||||||
Authors | Gaudier, M. / Gaudin, Y. / Knossow, M. | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: Crystal structure of vesicular stomatitis virus matrix protein. Authors: Gaudier, M. / Gaudin, Y. / Knossow, M. #1: Journal: Virology / Year: 2001 Title: Cleavage of Vesicular Stomatitis Virus Matrix Protein Prevents Self-association and Leads to Crystallization Authors: Gaudier, M. / Gaudin, Y. / Knossow, M. | ||||||
History |
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Remark 999 | SEQUENCE Author informed that protein sequence under study has not yet been deposited in any ... SEQUENCE Author informed that protein sequence under study has not yet been deposited in any sequence database |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lg7.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lg7.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 1lg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lg7_validation.pdf.gz | 435 KB | Display | wwPDB validaton report |
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Full document | 1lg7_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | 1lg7_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1lg7_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/1lg7 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/1lg7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21011.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vesicular stomatitis virus / Genus: Vesiculovirus / Strain: Indiana - Orsay / References: UniProt: Q8B0H2 |
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#2: 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: 2 Å3/Da / Density % sol: 38.55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 2000 monometylether, sodium chloride, sodium acetate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Gaudier, M., (2001) Virology, 288, 308. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 17, 1999 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→25 Å / Num. all: 210584 / Num. obs: 209741 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.069 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.96→2.01 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.41 / % possible all: 95.3 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 12771 / Num. measured all: 209741 / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS % possible obs: 95.3 % / Rmerge(I) obs: 0.41 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.96→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 44.7872 Å2 / ksol: 0.335821 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7033 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.03 Å / Total num. of bins used: 10
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Refinement | *PLUS Lowest resolution: 25 Å / Num. reflection obs: 12032 / Rfactor all: 0.218 / Rfactor obs: 0.206 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.327 / Rfactor Rwork: 0.239 / Rfactor obs: 0.239 |