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Yorodumi- PDB-2dkf: Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dkf | ||||||
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Title | Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily | ||||||
Components | metallo-beta-lactamase superfamily protein | ||||||
Keywords | HYDROLASE / beta-CASP family / metallo-beta-lactamase / ribonuclease / RNase E / Thermus thermophilus / 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 / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Ishikawa, I. / Nakagawa, N. / Kuramitsu, S. / Yokoyama, S. / Masui, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 2006 Title: Crystal structure of TTHA0252 from Thermus thermophilus HB8, a RNA degradation protein of the metallo-beta-lactamase superfamily Authors: Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dkf.cif.gz | 328.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dkf.ent.gz | 278.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/2dkf ftp://data.pdbj.org/pub/pdb/validation_reports/dk/2dkf | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 47446.340 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0252 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 55771634, UniProt: Q5SLP1*PLUS #2: Chemical | ChemComp-ZN / #3: 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: 3.2 Å3/Da / Density % sol: 61.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.0M Ammonium Sulfate, 1%(w/v) Polyethylene Glycol 3350, 0.1M Bis-Tris, 4%(v/v) 2,2,2 Trifluoroethanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.97882 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 7, 2005 |
Radiation | Monochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97882 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 58051 / Num. obs: 58051 / % possible obs: 99.5 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 9.95 / Num. unique all: 5799 / Rsym value: 0.281 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→19.99 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 68.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.013
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