+Open data
-Basic information
Entry | Database: PDB / ID: 2v7f | ||||||
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Title | Structure of P. abyssi RPS19 protein | ||||||
Components | RPS19E SSU RIBOSOMAL PROTEIN S19E | ||||||
Keywords | RIBOSOMAL PROTEIN / DIAMOND BLACKFAN ANEMIA SMALL RIBOSOMAL SUBUNIT | ||||||
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 / MIRAS / Resolution: 1.15 Å | ||||||
Authors | Gregory, L.A. / Aguissa-Toure, A.H. / Pinaud, N. / Legrand, P. / Gleizes, P.E. / Fribourg, S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2007 Title: Molecular Basis of Diamond Blackfan Anemia: Structure and Function Analysis of Rps19. Authors: Gregory, L.A. / Aguissa-Toure, A.H. / Pinaud, N. / Legrand, P. / Gleizes, P.E. / Fribourg, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v7f.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v7f.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 2v7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/2v7f ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v7f | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17422.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS ABYSSI (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) ROSETTA / References: UniProt: Q9V0G8 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 30% - 36% PEG 2000MME TRIS-HCL 100MM PH 6.8 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.984 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→28 Å / Num. obs: 49876 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.25 |
Reflection shell | Resolution: 1.15→1.25 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.12 / % possible all: 72.3 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 1.15→19.57 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.739 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / 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: 15.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→19.57 Å
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Refine LS restraints |
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