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Yorodumi- PDB-2czw: Crystal structure analysis of protein component Ph1496p of P.hori... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2czw | ||||||
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Title | Crystal structure analysis of protein component Ph1496p of P.horikoshii ribonuclease P | ||||||
Components | 50S ribosomal protein L7AeRibosome | ||||||
Keywords | RIBOSOME / HYDROLASE / ribonuclease P / ribonucleoprotein | ||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Fukuhara, H. / Kifusa, M. / Watanabe, M. / Terada, A. / Honda, T. / Numata, T. / Kakuta, Y. / Kimura, M. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2006 Title: A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3 Authors: Fukuhara, H. / Kifusa, M. / Watanabe, M. / Terada, A. / Honda, T. / Numata, T. / Kakuta, Y. / Kimura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2czw.cif.gz | 36.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2czw.ent.gz | 24.4 KB | Display | PDB format |
PDBx/mmJSON format | 2czw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/2czw ftp://data.pdbj.org/pub/pdb/validation_reports/cz/2czw | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 13573.874 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: ph1496 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / References: UniProt: P62009 |
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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: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: PEG 3000, CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9792 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 12, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 12373 / Num. obs: 12373 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.7→1.76 Å / % possible all: 74.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→23.5 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→23.5 Å
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Refine LS restraints |
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