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Open data
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Basic information
Entry | Database: PDB / ID: 1n93 | ||||||
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Title | Crystal Structure of the Borna Disease Virus Nucleoprotein | ||||||
![]() | p40 nucleoprotein | ||||||
![]() | VIRAL PROTEIN / RNA virus nucleoprotein tetramer | ||||||
Function / homology | ![]() : / symbiont-mediated arrest of host cell cycle during G2/M transition / : / helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rudolph, M.G. / Kraus, I. / Dickmanns, A. / Garten, W. / Ficner, R. | ||||||
![]() | ![]() Title: Crystal structure of the Borna Disease Virus nucleoprotein Authors: Rudolph, M.G. / Kraus, I. / Dickmanns, A. / Eickmann, M. / Garten, W. / Ficner, R. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The authors state that the crystallographic data strongly support a tetramer. The authors can not confirm this at present, since there are no independent data published as to the oligomeric state of the protein in solution. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.6 KB | Display | ![]() |
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PDB format | ![]() | 63.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.6 KB | Display | ![]() |
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Full document | ![]() | 428.7 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41509.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.43 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: PEG 550 MME, NaCl, DTT, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 18, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8841 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 50437 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 23.87 Å2 / Rsym value: 0.108 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3 / Num. unique all: 4392 / Rsym value: 0.426 / % possible all: 86.5 |
Reflection | *PLUS Lowest resolution: 41.7 Å / Rmerge(I) obs: 0.108 |
Reflection shell | *PLUS % possible obs: 86.5 % / Num. unique obs: 4392 / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 4.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: none Resolution: 1.76→29.23 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.721 / SU ML: 0.055 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.09 / ESU R Free: 0.088 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.531 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→29.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.806 Å / Total num. of bins used: 20
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Refinement | *PLUS Lowest resolution: 29.2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.187 / Rfactor Rwork: 0.163 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.76 Å / Lowest resolution: 1.81 Å |