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Yorodumi- PDB-1uty: Crystal structure of the RNA binding domain of Bluetongue virus n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uty | ||||||
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Title | Crystal structure of the RNA binding domain of Bluetongue virus non-structural protein 2(NS2) | ||||||
Components | NON-STRUCTURAL PROTEIN 2 | ||||||
Keywords | VIRAL PROTEIN / RNA BINDING PROTEIN | ||||||
Function / homology | Bluetongue virus nonstructural protein NS2 / NS2, N-terminal / Bluetongue virus non-structural protein NS2 / RNA binding / Non-structural protein NS2 Function and homology information | ||||||
Biological species | BLUETONGUE VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Butan, C. / Van Der zandt, H. / Tucker, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structure and Assembly of the RNA Binding Domain of Bluetongue Virus Non-Structural Protein 2 Authors: Butan, C. / Van Der Zandt, H. / Tucker, P. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uty.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uty.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 1uty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uty_validation.pdf.gz | 376.4 KB | Display | wwPDB validaton report |
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Full document | 1uty_full_validation.pdf.gz | 379.9 KB | Display | |
Data in XML | 1uty_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 1uty_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/1uty ftp://data.pdbj.org/pub/pdb/validation_reports/ut/1uty | 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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Unit cell |
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-Components
#1: Protein | Mass: 21361.625 Da / Num. of mol.: 2 / Fragment: RNA BINDING DOMAIN, RESIDUES 1-177 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BLUETONGUE VIRUS / Strain: 8 / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: P23065, RNA-directed RNA polymerase #2: Water | ChemComp-HOH / | Compound details | FUNCTION: RNA BINDING PROTEIN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 53 % |
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Crystal grow | pH: 7.5 Details: 20% JEFFAMINE M-600 PH 7.6, 0.65 M NACL, 10 MM SODIUM PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 15, 2001 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.803 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 18244 / % possible obs: 99.9 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 34.57 |
Reflection shell | Resolution: 2.4→2.46 Å / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 6.6 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.951 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 24.73 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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