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- PDB-3p2j: Crystal structure of peptidyl-tRNA hydrolase from Mycobacterium s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3p2j | ||||||
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Title | Crystal structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis at 2.2 A resolution | ||||||
![]() | Peptidyl-tRNA hydrolase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kumar, A. / Singh, A. / Yadav, R. / Sinha, M. / Arora, A. / Sharma, S. / Singh, T.P. | ||||||
![]() | ![]() Title: Crystal Structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis at 2.2 A resolution Authors: Kumar, A. / Singh, A. / Yadav, R. / Sinha, M. / Arora, A. / Sharma, S. / Singh, T.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.2 KB | Display | ![]() |
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PDB format | ![]() | 36.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.2 KB | Display | ![]() |
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Full document | ![]() | 427.6 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3kjzS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20270.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | AUTHOR STATED THAT THERE WERE ERRORS IN THE SEQUENCE DATABASE, THE SEQUENCE IN THIS ENTRY ...AUTHOR STATED THAT THERE WERE ERRORS IN THE SEQUENCE DATABASE, THE SEQUENCE IN THIS ENTRY REPRESENTE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.09 % |
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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, 10% isopropanol, 30% PEG 1500, 5mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 2009 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.514 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→42.67 Å / Num. all: 8170 / Num. obs: 8170 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 32.3 Å2 / Rsym value: 0.078 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.22→2.3 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.641 / % possible all: 89.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3KJZ Resolution: 2.22→14.96 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.226 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.27 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.22→14.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.224→2.282 Å / Total num. of bins used: 20
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