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Yorodumi- PDB-2r72: Crystal structure of infectious bursal disease virus VP1 polymera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r72 | ||||||
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Title | Crystal structure of infectious bursal disease virus VP1 polymerase, incubated with Mg2+ ion. | ||||||
Components | INFECTIOUS BURSAL DISEASE VIRUS VP1 POLYMERASE | ||||||
Keywords | TRANSFERASE / IBDV / infectious bursal disease virus / birnavirus / VP1 / polymerase / magnesium / mg | ||||||
Function / homology | Function and homology information viral genome replication / virion component / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTP binding Similarity search - Function | ||||||
Biological species | Infectious bursal disease virus (Gumboro virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 Å | ||||||
Authors | Garriga, D. / Navarro, A. / Querol-Audi, J. / Abaitua, F. / Rodriguez, J.F. / Verdaguer, N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Activation mechanism of a noncanonical RNA-dependent RNA polymerase. Authors: Garriga, D. / Navarro, A. / Querol-Audi, J. / Abaitua, F. / Rodriguez, J.F. / Verdaguer, N. | ||||||
History |
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Remark 999 | Sequence The sequence is not available in the UniProt database at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r72.cif.gz | 159.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r72.ent.gz | 122.8 KB | Display | PDB format |
PDBx/mmJSON format | 2r72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/2r72 ftp://data.pdbj.org/pub/pdb/validation_reports/r7/2r72 | HTTPS FTP |
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-Related structure data
Related structure data | 2pusSC 2r70C 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: 94651.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Infectious bursal disease virus (Gumboro virus) Genus: Avibirnavirus / Strain: Soroa / Gene: VP1 polymerase (segment B) / Cell (production host): HighFive cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Q6Q5 | ||
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#2: Chemical | #3: 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: 4.08 Å3/Da / Density % sol: 69.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% PEG 3350, 0.4M LiNO3, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.15→36.664 Å / Num. all: 27660 / Num. obs: 27660 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 5.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PUS Resolution: 3.15→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.894 / SU B: 35.261 / SU ML: 0.277 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.048 / ESU R Free: 0.362 / 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: 63.897 Å2
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Refinement step | Cycle: LAST / Resolution: 3.15→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.23 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -28.7939 Å / Origin y: -36.4306 Å / Origin z: 111.5113 Å
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