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Yorodumi- PDB-2dyi: Crystal structure of 16S ribosomal RNA processing protein RimM fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dyi | ||||||
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Title | Crystal structure of 16S ribosomal RNA processing protein RimM from Thermus thermophilus HB8 | ||||||
Components | Probable 16S rRNA-processing protein rimM | ||||||
Keywords | RIBOSOME / ribosomal protein S19 / 16S rRNA processing / PRC-barrel / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information rRNA processing / ribosomal small subunit biogenesis / ribosome binding / ribosome / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kawazoe, M. / Takemoto, C. / Kaminishi, T. / Tatsuguchi, A. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Crystal structure of 16S ribosomal RNA processing protein RimM from Thermus thermophilus HB8 Authors: Kawazoe, M. / Takemoto, C. / Kaminishi, T. / Tatsuguchi, A. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dyi.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dyi.ent.gz | 32.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dyi_validation.pdf.gz | 421.2 KB | Display | wwPDB validaton report |
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Full document | 2dyi_full_validation.pdf.gz | 421.6 KB | Display | |
Data in XML | 2dyi_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 2dyi_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/2dyi ftp://data.pdbj.org/pub/pdb/validation_reports/dy/2dyi | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18094.768 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1033 / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJH5 |
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#2: 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: 2.65 Å3/Da / Density % sol: 53.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 25mM Tris-HCl, 0.025% w/v Polyethylene glycol 6000, 0.5M Lithium sulfate, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 15, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.4 Å / Num. obs: 13576 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.17 % / Biso Wilson estimate: 6.9 Å2 / Rsym value: 0.083 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 6.93 / Num. unique all: 1316 / Rsym value: 0.314 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Preliminary assigned NMR model Resolution: 2→42.4 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1166587.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.9156 Å2 / ksol: 0.374585 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→42.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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