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Yorodumi- PDB-3kk0: Crystal structure of partially folded intermediate state of pepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kk0 | ||||||
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Title | Crystal structure of partially folded intermediate state of peptidyl-tRNA hydrolase from Mycobacterium smegmatis | ||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | ||||||
Keywords | HYDROLASE / Protein synthesis | ||||||
Function / homology | Function and homology information peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Kumar, A. / Singh, N. / Yadav, R. / Sharma, S. / Arora, A. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Structures of Fully-Folded Native and Partially-Folded Intermediate States of Peptidyl-tRNA Hydrolase from Mycobacterium smegmatis Authors: Kumar, A. / Singh, N. / Yadav, R. / Sharma, S. / Arora, A. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kk0.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kk0.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 3kk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/3kk0 ftp://data.pdbj.org/pub/pdb/validation_reports/kk/3kk0 | HTTPS FTP |
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-Related structure data
Related structure data | 3kjzS S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 20270.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A0R3D3, peptidyl-tRNA hydrolase |
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-Non-polymers , 5 types, 179 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-BME / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THERE ARE CONFLICTS BETWEEN THE REPORTED SEQUENCE AND DATABASE REFERENCE SEQUENCE. THE DEPOSITORS ...THERE ARE CONFLICTS BETWEEN THE REPORTED SEQUENCE AND DATABASE REFERENCE SEQUENCE. THE DEPOSITORS |
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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: 2.78 Å3/Da / Density % sol: 55.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20mM Tris-HCl, 1mM EDTA, 50mM NaCl, 5mM 2-mercaptoethanol, 5% (w/v) PEG 400, 10% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 13, 2009 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→25.99 Å / Num. all: 6932 / Num. obs: 6733 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 52.1 Å2 |
Reflection shell | Resolution: 2.65→2.7 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KJZ Resolution: 2.65→25.99 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 79196.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 148.192 Å2 / ksol: 0.241404 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.18 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→25.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.82 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
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Xplor file |
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