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Yorodumi- PDB-3tcn: Crystal structures of Peptidyl-tRNA hydrolase from Mycobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tcn | ||||||
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Title | Crystal structures of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis - Form 2 grown in presence of Pentaglycine | ||||||
Components | Peptidyl-tRNA hydrolase | ||||||
Keywords | HYDROLASE / Pth / Hydrolysis of Peptidyl-tRNA / Peptidyl-tRNA / Cytosol | ||||||
Function / homology | Function and homology information peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Selvaraj, M. / Ahmad, R. / Varshney, U. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Structures of new crystal forms of Mycobacterium tuberculosis peptidyl-tRNA hydrolase and functionally important plasticity of the molecule Authors: Selvaraj, M. / Ahmad, R. / Varshney, U. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tcn.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tcn.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 3tcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/3tcn ftp://data.pdbj.org/pub/pdb/validation_reports/tc/3tcn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20485.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT1042, MTCY10G2.35, pth, Rv1014c / Plasmid: pRSETBMtuPth / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P65865, UniProt: P9WHN7*PLUS, peptidyl-tRNA hydrolase #2: 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: 1.92 Å3/Da / Density % sol: 35.85 % |
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Crystal grow | Temperature: 291 K / Method: microbatch under oil / pH: 7.5 Details: 0.1M HEPES, 15% PEG 8000, 5% isopropanol, pH 7.5, Microbatch under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 4, 2009 / Details: Osmic mirrors |
Radiation | Monochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→60 Å / Num. obs: 13866 / % possible obs: 100 % / Redundancy: 4 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.13 |
Reflection shell | Resolution: 2.3→2.42 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 42.9736 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.61 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.42 Å | ||||||||||||||||||||||||||||
Xplor file |
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