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Yorodumi- PDB-3erj: Crystal structure of the peptidyl-tRNA hydrolase AF2095 from Arch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3erj | ||||||
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Title | Crystal structure of the peptidyl-tRNA hydrolase AF2095 from Archaeglobus fulgidis. Northeast Structural Genomics Consortium target GR4 | ||||||
Components | Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B | ||||||
Keywords | HYDROLASE / alpha-beta / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Cytoplasm | ||||||
Function / homology | Function and homology information positive regulation of anoikis / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / negative regulation of anoikis / translation / cytosol Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Forouhar, F. / Su, M. / Seetharaman, J. / Conover, K. / Janjua, H. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Cooper, B. / Baran, M.C. ...Forouhar, F. / Su, M. / Seetharaman, J. / Conover, K. / Janjua, H. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Cooper, B. / Baran, M.C. / Liu, J. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the peptidyl-tRNA hydrolase AF2095 from Archaeglobus fulgidis. Northeast Structural Genomics Consortium target GR4 Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Conover, K. / Janjua, H. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Cooper, B. / Baran, M.C. / Liu, J. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3erj.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3erj.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 3erj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/3erj ftp://data.pdbj.org/pub/pdb/validation_reports/er/3erj | HTTPS FTP |
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-Related structure data
Related structure data | 1rlkS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13578.943 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF2095, AF_2095, pth / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O28185, 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: 2 Å3/Da / Density % sol: 38.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM Tris (pH 8), 20% PEG3350, 200 mM NaCl, and 0.5% w/v polyvinylpyrrolidone K15 , VAPOR ...Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM Tris (pH 8), 20% PEG3350, 200 mM NaCl, and 0.5% w/v polyvinylpyrrolidone K15 , VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97877 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 30, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97877 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 38938 / Num. obs: 38783 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.043 / Net I/σ(I): 34.46 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 4.45 / Num. unique all: 3798 / Rsym value: 0.233 / % possible all: 97.5 |
-Processing
Software | Name: CNS / Version: 1.2 / Classification: refinement | |||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RLK Resolution: 1.8→19.88 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 114421.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.7469 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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