+Open data
-Basic information
Entry | Database: PDB / ID: 2pth | ||||||
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Title | PEPTIDYL-TRNA HYDROLASE FROM ESCHERICHIA COLI | ||||||
Components | PEPTIDYL-TRNA HYDROLASEAlternative ribosome-rescue factor B | ||||||
Keywords | HYDROLASE / PEPTIDYL-TRNA | ||||||
Function / homology | Function and homology information peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / protein quality control for misfolded or incompletely synthesized proteins / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRS / Resolution: 1.2 Å | ||||||
Authors | Schmitt, E. / Mechulam, Y. / Fromant, M. / Plateau, P. / Blanquet, S. | ||||||
Citation | Journal: EMBO J. / Year: 1997 Title: Crystal structure at 1.2 A resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase. Authors: Schmitt, E. / Mechulam, Y. / Fromant, M. / Plateau, P. / Blanquet, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pth.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pth.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 2pth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/2pth ftp://data.pdbj.org/pub/pdb/validation_reports/pt/2pth | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20982.115 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: CYTOPLASM / Gene: PTH / Plasmid: PUC18 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P0A7D1, peptidyl-tRNA hydrolase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.05 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 10% PEG6000,12% ISOPROPANOL, 0,1 M TRIS-CL PH7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 6 ℃ / Method: vapor diffusion, hanging dropDetails: Schmitt, E., (1997) Proteins.Struct.Funct.Genet., 28, 135. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.994 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.994 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→28 Å / Num. obs: 55575 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 12.7 Å2 / Rsym value: 0.046 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.15 / % possible all: 85.3 |
Reflection | *PLUS Rmerge(I) obs: 0.046 |
-Processing
Software |
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Refinement | Method to determine structure: MIRS / Resolution: 1.2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: SOME WATER MOLECULES ARE IN CLOSE CONTACT. THESE MOLECULES SHOULD BE CONSIDERED AS ALTERNATE POSITIONS, NOT PRESENT SIMULTANEOUSLY IN THE ASYMMETRIC UNIT.
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Displacement parameters | Biso mean: 17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.25 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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