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Yorodumi- PDB-2e0y: Crystal structure of the samarium derivative of mature gamma-glut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e0y | ||||||
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Title | Crystal structure of the samarium derivative of mature gamma-glutamyltranspeptidase from Escherichia coli | ||||||
Components | (Gamma-glutamyltranspeptidase) x 2 | ||||||
Keywords | TRANSFERASE / gamma-glutamyltransferase / ggt / gamma-gt / glutathione | ||||||
Function / homology | Function and homology information amino acid salvage / gamma-glutamyl-peptidase activity / gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / glutathione biosynthetic process / self proteolysis / outer membrane-bounded periplasmic space / periplasmic space Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.02 Å | ||||||
Authors | Okada, T. / Wada, K. / Fukuyama, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal structure of the gamma-glutamyltranspeptidase precursor protein from Escherichia coli. Structural changes upon autocatalytic processing and implications for the maturation mechanism Authors: Okada, T. / Suzuki, H. / Wada, K. / Kumagai, H. / Fukuyama, K. #1: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Crystal structures of gamma-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate Authors: Okada, T. / Suzuki, H. / Wada, K. / Kumagai, H. / Fukuyama, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e0y.cif.gz | 226.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e0y.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 2e0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e0y_validation.pdf.gz | 467.2 KB | Display | wwPDB validaton report |
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Full document | 2e0y_full_validation.pdf.gz | 484.9 KB | Display | |
Data in XML | 2e0y_validation.xml.gz | 45.6 KB | Display | |
Data in CIF | 2e0y_validation.cif.gz | 65.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/2e0y ftp://data.pdbj.org/pub/pdb/validation_reports/e0/2e0y | HTTPS FTP |
-Related structure data
Related structure data | 2e0wC 2e0xC 2dbuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39827.070 Da / Num. of mol.: 2 / Fragment: LARGE SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ggt / Plasmid: PSH1291 / Production host: Escherichia coli (E. coli) / Strain (production host): SH1603 / References: UniProt: P18956, gamma-glutamyltransferase #2: Protein | Mass: 20262.951 Da / Num. of mol.: 2 / Fragment: SMALL SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ggt / Plasmid: PSH1291 / Production host: Escherichia coli (E. coli) / Strain (production host): SH1603 / References: UniProt: P18956, gamma-glutamyltransferase #3: Chemical | ChemComp-GOL / #4: Chemical | #5: 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: 2.66 Å3/Da / Density % sol: 53.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15% PEG 4000, 0.2M calcium chloride, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.2 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2005 |
Radiation | Monochromator: SI(111) DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 84609 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.065 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 5.1 % / Num. unique all: 16196 / Rsym value: 0.285 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2DBU Resolution: 2.02→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 71919.617 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.254 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.02→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.15 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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