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- PDB-4hiy: crystal structure of R34/53A, D95N, H112W mutant of borna disease... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hiy | ||||||
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Title | crystal structure of R34/53A, D95N, H112W mutant of borna disease virus matrix protein | ||||||
![]() | Matrix protein | ||||||
![]() | VIRAL PROTEIN / VIRAL MATRIX PROTEIN / RNA BINDING / MEMBRANE BINDING / VIRUSES / SSRNA / NEGATIVE-STRAND VIRUSES / MONONEGAVIRALES / BORNAVIRIDAE / BORNA VIRUS / VIRION | ||||||
Function / homology | ![]() virion component / host cell cytoplasm / structural constituent of virion / host cell plasma membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dautel, P. / Kolenko, P. / Stubbs, M.T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.8 KB | Display | ![]() |
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PDB format | ![]() | 28.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.2 KB | Display | ![]() |
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Full document | ![]() | 424.5 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hi5C ![]() 4hitC ![]() 4hiuC ![]() 4hiwC ![]() 3f1jS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16152.665 Da / Num. of mol.: 1 / Mutation: R34A, R53A, D95N, H112W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.125 Li2SO4, 25% GLYCEROL, 0.075 HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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→56 Å / Num. all: 3517 / Num. obs: 3517 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 11.2 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3.3→3.48 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 3.2 / Num. unique all: 493 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3F1J Resolution: 3.31→56 Å / Cor.coef. Fo:Fc: 0.94 / SU B: 14.355 / SU ML: 0.233 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: R VALUE (WORKING SET) = 0.175; FREE R = 0. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: R VALUE (WORKING SET) = 0.175; FREE R = 0.233 FROM A RANDOM TEST SET COMPRISING 5% OF REFLECTIONS (157 TOTAL). FINAL REFINEMENT WAS PERFORMED USING ALL REFLECTIONS.
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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: 64.838 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.31→56 Å
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Refine LS restraints |
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