+Open data
-Basic information
Entry | Database: PDB / ID: 6ydr | ||||||
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Title | Crystal structure of Mengla Virus VP30 C-terminal domain | ||||||
Components | Minor nucleoprotein VP30 | ||||||
Keywords | VIRAL PROTEIN / Transcription Factor | ||||||
Function / homology | Function and homology information viral nucleocapsid / host cell cytoplasm / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mengla dianlovirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Tomas Gilabert, O. / Ferrero, D.S. / Verdaguer, N. | ||||||
Funding support | Spain, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Mengla Virus VP30 C-terminal domain Authors: Tomas Gilabert, O. / Ferrero, D.S. / Verdaguer, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ydr.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ydr.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ydr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/6ydr ftp://data.pdbj.org/pub/pdb/validation_reports/yd/6ydr | HTTPS FTP |
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-Related structure data
Related structure data | 5t3wS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16747.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mengla dianlovirus / Gene: VP30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A3S8UVN5 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium Sulfate , 0.1M Sodium, Acetate pH4.6, 25% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→40.87 Å / Num. obs: 36367 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.06541 / Rpim(I) all: 0.03027 / Rrim(I) all: 0.07254 / Net I/σ(I): 16.27 |
Reflection shell | Resolution: 1.344→1.392 Å / Rmerge(I) obs: 0.4376 / Mean I/σ(I) obs: 2.82 / Num. unique obs: 3598 / CC1/2: 0.852 / CC star: 0.959 / Rpim(I) all: 0.2158 / Rrim(I) all: 0.4909 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T3W Resolution: 1.34→40.87 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.185 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.282 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→40.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.344→1.379 Å / Total num. of bins used: 20
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