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Yorodumi- PDB-3k4t: Crystal structure of the virion-associated protein P3 from caulim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k4t | ||||||
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Title | Crystal structure of the virion-associated protein P3 from caulimovirus | ||||||
Components | Virion-associated protein | ||||||
Keywords | VIRAL PROTEIN / DNA-BINDING PROTEIN / COILED-COIL / TETRAMER / PROTEIN BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cauliflower mosaic virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Dumas, C. / Hoh, F. | ||||||
Citation | Journal: J.Virol. / Year: 2010 Title: Structural insights into the molecular mechanisms of cauliflower mosaic virus transmission by its insect vector. Authors: Hoh, F. / Uzest, M. / Drucker, M. / Plisson-Chastang, C. / Bron, P. / Blanc, S. / Dumas, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k4t.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k4t.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 3k4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/3k4t ftp://data.pdbj.org/pub/pdb/validation_reports/k4/3k4t | HTTPS FTP |
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-Related structure data
Related structure data | 3f6nSC 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: 10489.141 Da / Num. of mol.: 4 / Fragment: UNP residues 1-95 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cauliflower mosaic virus (STRAIN STRASBOURG) Strain: STRASBOURG / Gene: ORF III / Plasmid: PET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P03551 #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.92 % |
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Crystal grow | Temperature: 291 K / pH: 6.5 Details: 25% PEG 1000, 0.1M MES-NAOH BUFFER, 1.2 MOLAR-EXCESS DNA OLIGONUCLEOTIDE (POLY-AT, 14 BP) , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97925 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→18.98 Å / Num. obs: 9317 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 60.1 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.084 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.59→2.74 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.345 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3F6N Resolution: 2.59→18.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 33.25 / SU ML: 0.311 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS REFINEMENT 4 GROUPS / Cross valid method: THROUGHOUT / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: WEIGHT MATRIX 0.035
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→18.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.65 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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