+Open data
-Basic information
Entry | Database: PDB / ID: 2v94 | ||||||
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Title | Crystal structure of P. abyssi RPS24 | ||||||
Components | 30S RIBOSOMAL PROTEIN S24ERibosome | ||||||
Keywords | RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN | ||||||
Function / homology | Function and homology information ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation Similarity search - Function | ||||||
Biological species | PYROCOCCUS ABYSSI (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Legrand, P. / Pinaud, N. / Gleizes, P.E. / Fribourg, S. | ||||||
Citation | Journal: Hum.Mol.Genet. / Year: 2008 Title: Mutation of Ribosomal Protein Rps24 in Diamond- Blackfan Anemia Results in a Ribosome Biogenesis Disorder. Authors: Choesmel, V. / Fribourg, S. / Aguissa-Toure, A.H. / Pinaud, N. / Legrand, P. / Gazda, H.T. / Gleizes, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v94.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v94.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 2v94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/2v94 ftp://data.pdbj.org/pub/pdb/validation_reports/v9/2v94 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 13026.407 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS ABYSSI (archaea) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q9UY20 #2: 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: 3.04 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 4.2 / Details: 100MM NA ACETATE 40% PEG 400 185MM MGCL2, pH 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 5, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 13468 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.8 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.9→27.39 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.878 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.156 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→27.39 Å
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Refine LS restraints |
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