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Yorodumi- PDB-4l8h: Bacteriophage Qbeta coat protein in complex with RNA operator hairpin -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l8h | ||||||
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Title | Bacteriophage Qbeta coat protein in complex with RNA operator hairpin | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Alpha Beta 2-Layer Sandwich / Levivirus coat protein / Structural / Translational repressor / RNA binding / Virion | ||||||
Function / homology | Function and homology information T=3 icosahedral viral capsid / translation repressor activity / structural molecule activity / RNA binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage Qbeta (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Rumnieks, J. / Tars, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Crystal structure of the bacteriophage q beta coat protein in complex with the RNA operator of the replicase gene. Authors: Rumnieks, J. / Tars, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l8h.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l8h.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 4l8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/4l8h ftp://data.pdbj.org/pub/pdb/validation_reports/l8/4l8h | HTTPS FTP |
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-Related structure data
Related structure data | 1qbeS 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
#1: Protein | Mass: 14147.862 Da / Num. of mol.: 2 / Mutation: P42R,C74G,C80G,N129R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage Qbeta (virus) / Gene: coat / Plasmid: pET28-Qb150 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03615 #2: RNA chain | | Mass: 6391.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical synthesis #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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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: 3.63 Å3/Da / Density % sol: 66.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M sodium acetate, 0.2 M zinc acetate, 9% PEG 3000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2013 / Details: multilayer mirrors |
Radiation | Monochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40.064 Å / Num. all: 21342 / Num. obs: 21342 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.937 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1QBE Resolution: 2.4→37.63 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.871 / SU B: 7.266 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.242 / 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: 34.194 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→37.63 Å
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Refine LS restraints |
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