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Yorodumi- PDB-2naf: Solution structure of peptidyl-tRNA hydrolase from Mycobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2naf | ||||||
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Title | Solution structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis | ||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | ||||||
Keywords | HYDROLASE / Protein | ||||||
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 | SOLUTION NMR / molecular dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Yadav, R. / Pathak, P. / Fatma, F. / Kabra, A. / Pulavarti, S. / Jain, A. / Kumar, A. / Shukla, V. / Arora, A. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2016 Title: Structural characterization of peptidyl-tRNA hydrolase from Mycobacterium smegmatis by NMR spectroscopy. Authors: Kabra, A. / Fatma, F. / Shahid, S. / Pathak, P.P. / Yadav, R. / Pulavarti, S.V. / Tripathi, S. / Jain, A. / Arora, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2naf.cif.gz | 647.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2naf.ent.gz | 555.6 KB | Display | PDB format |
PDBx/mmJSON format | 2naf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/2naf ftp://data.pdbj.org/pub/pdb/validation_reports/na/2naf | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 20306.324 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 / Gene: MSMEG_5432, MSMEI_5283, pth / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R3D3, peptidyl-tRNA hydrolase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | |||||||||||||||
NMR constraints | NOE constraints total: 2352 / Hydrogen bond constraints total count: 73 / Protein chi angle constraints total count: 17 / Protein phi angle constraints total count: 137 / Protein psi angle constraints total count: 135 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 10 |