+Open data
-Basic information
Entry | Database: PDB / ID: 3v7q | ||||||
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Title | Crystal structure of B. subtilis YlxQ at 1.55 A resolution | ||||||
Components | Probable ribosomal protein ylxQ | ||||||
Keywords | RNA BINDING PROTEIN / L7Ae superfamily / K-turn binding / K-turn RNA / Hypothetical ribosomal protein | ||||||
Function / homology | Function and homology information ribosome biogenesis / ribosome / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Baird, N.J. / Zhang, J. / Hamma, T. / Ferre-D'Amare, A.R. | ||||||
Citation | Journal: Rna / Year: 2012 Title: YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. Authors: Baird, N.J. / Zhang, J. / Hamma, T. / Ferre-D'Amare, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v7q.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v7q.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 3v7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/3v7q ftp://data.pdbj.org/pub/pdb/validation_reports/v7/3v7q | HTTPS FTP |
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-Related structure data
Related structure data | 3v7eC 3on1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 11128.995 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU16620, rplGA, ylxQ, ymxC / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P32729 #2: Chemical | #3: Chemical | #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: 2.18 Å3/Da / Density % sol: 43.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M ammonium acetate pH 7.0, 0.1 M sodium citrate pH 5.6, and 30% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 10, 2010 |
Radiation | Monochromator: Asymmetric curved crystal of Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 42151 / Num. obs: 41302 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.6 Å2 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 5.5 % / Num. unique all: 4152 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3on1 Resolution: 1.55→19.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 149294.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.8237 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→19.97 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.56 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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