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Yorodumi- PDB-4hiu: Crystal structure of R34/53A mutant of borna disease virus matrix... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hiu | ||||||
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Title | Crystal structure of R34/53A mutant of borna disease virus matrix protein | ||||||
Components | Matrix protein | ||||||
Keywords | VIRAL PROTEIN / VIRAL MATRIX PROTEIN / RNA BINDING / MEMBRANE BINDING / VIRUSES / SSRNA / NEGATIVE-STRAND VIRUSES / MONONEGAVIRALES / BORNAVIRIDAE / BORNA VIRUS / VIRION | ||||||
Function / homology | Function and homology information virion component / host cell cytoplasm / structural constituent of virion / host cell plasma membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Borna disease virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Dautel, P. / Kolenko, P. / Stubbs, M.T. | ||||||
Citation | Journal: To be Published Title: Matrix protein variants provide support for alternative borna disease virus infection pathway Authors: Dautel, P. / Kolenko, P. / Stubbs, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hiu.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hiu.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 4hiu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hiu_validation.pdf.gz | 957.1 KB | Display | wwPDB validaton report |
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Full document | 4hiu_full_validation.pdf.gz | 958.1 KB | Display | |
Data in XML | 4hiu_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 4hiu_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/4hiu ftp://data.pdbj.org/pub/pdb/validation_reports/hi/4hiu | HTTPS FTP |
-Related structure data
Related structure data | 4hi5C 4hitC 4hiwC 4hiyC 3f1jS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 16105.587 Da / Num. of mol.: 1 / Mutation: R34A, R53A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borna disease virus / Gene: M / Plasmid: PMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0C794 |
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#2: Chemical | ChemComp-C5P / |
#3: Chemical | ChemComp-5GP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.09 M NPS buffer, 30% GLYCEROL, PEG4000, 0.1 M HEPES (MOPS), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 3751 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 11 % / Biso Wilson estimate: 93 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 3.3→3.48 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3F1J Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.935 / SU B: 14.243 / SU ML: 0.229 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.303→3.388 Å / Total num. of bins used: 20 /
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