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Yorodumi- PDB-2qj1: Crystal structure of infectious bursal disease virus VP1 polymera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qj1 | ||||||
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Title | Crystal structure of infectious bursal disease virus VP1 polymerase incubated with an oligopeptide mimicking the VP3 C-terminus | ||||||
Components | Infectious bursal disease virus VP1 polymerase | ||||||
Keywords | TRANSFERASE / infectious bursal disease virus / ibdv / birnavirus / polymerase / vp1 / vp3 / activation | ||||||
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 / Resolution: 3.48 Å | ||||||
Authors | Garriga, D. / Navarro, A. / Querol-Audi, J. / Abaitua, F. / Rodriguez, J.F. / Verdaguer, N. | ||||||
Citation | Journal: To be Published Title: Unprecedented activation mechanism of a non-canonical 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 400 | COMPOUND THE VP3 PEPTIDE WAS CRYSTALLIZED WITH THE VP1 PROTEIN, BUT IT APPEARS POORLY ORDERED IN ...COMPOUND THE VP3 PEPTIDE WAS CRYSTALLIZED WITH THE VP1 PROTEIN, BUT IT APPEARS POORLY ORDERED IN THE STRUCTURE OF THE COMPLEX, AS ONLY A WEAK ELONGATED EXTRA DENSITY WAS DETECTED. THIS DENSITY COULD BE INTERPRETED AS DUE TO THE PRESENCE OF ABOUT FIVE AMINO ACIDS IN AN EXTENDED CONFORMATION, BUT THE AUTHORS WERE NOT ABLE TO ASSIGN ANY RESIDUE TO IT. | ||||||
Remark 999 | SEQUENCE AUTHORS STATE THAT RESIDUE AT POSITION 4 IS INDEED VALINE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qj1.cif.gz | 159.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qj1.ent.gz | 123.8 KB | Display | PDB format |
PDBx/mmJSON format | 2qj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qj1_validation.pdf.gz | 431 KB | Display | wwPDB validaton report |
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Full document | 2qj1_full_validation.pdf.gz | 453.5 KB | Display | |
Data in XML | 2qj1_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 2qj1_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/2qj1 ftp://data.pdbj.org/pub/pdb/validation_reports/qj/2qj1 | HTTPS FTP |
-Related structure data
Related structure data | 2pusS S: Starting model for refinement |
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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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Details | This molecule is a monomer. |
-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 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five (TM) cells / References: UniProt: Q82629, UniProt: Q9Q6Q5*PLUS |
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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: 4.07 Å3/Da / Density % sol: 69.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 10-12% PEG 3350, 0.3-0.5M LiNO3, pH 6.5-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: 3.48→40 Å / Num. all: 20344 / Num. obs: 20344 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.11 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 3.5→3.65 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.54 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: VP1 polymease apo form structure (PDB code 2PUS) Resolution: 3.48→19.98 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.852 / SU B: 59.429 / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.558 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.518 Å2
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Refinement step | Cycle: LAST / Resolution: 3.48→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.484→3.572 Å / Total num. of bins used: 20
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