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Yorodumi- PDB-3iek: Crystal Structure of native TTHA0252 from Thermus thermophilus HB8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iek | ||||||
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Title | Crystal Structure of native TTHA0252 from Thermus thermophilus HB8 | ||||||
Components | Ribonuclease TTHA0252 | ||||||
Keywords | HYDROLASE / metallo beta lactamase fold / Endonuclease / Metal-binding / Nuclease / RNA-binding / rRNA processing | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Yokoyama, S. / Masui, R. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of native TTHA0252 from Thermus thermophilus HB8 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 | 3iek.cif.gz | 359.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iek.ent.gz | 294.1 KB | Display | PDB format |
PDBx/mmJSON format | 3iek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/3iek ftp://data.pdbj.org/pub/pdb/validation_reports/ie/3iek | HTTPS FTP |
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-Related structure data
Related structure data | 2dkfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 47118.074 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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5SLP1, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-ZN / #5: 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: 3.15 Å3/Da / Density % sol: 60.89 % / Mosaicity: 0.306 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 50mM sodium citrate, 0.2M ammonium sulfate, 0.6M lithium sulfate, pH 5.6, 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: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 26, 2009 |
Radiation | Monochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 144351 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.057 / Χ2: 1.191 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.375 / Num. unique all: 14217 / Χ2: 0.947 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DKF Resolution: 2.05→50 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 48.524 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.1 Å2 / Biso mean: 39.268 Å2 / Biso min: 9.14 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.006
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Xplor file |
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