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Yorodumi- PDB-2e0x: Crystal Structure of Gamma-glutamyltranspeptidase from Escherichi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e0x | ||||||
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Title | Crystal Structure of Gamma-glutamyltranspeptidase from Escherichia coli (monoclinic form) | ||||||
Components | (Gamma-glutamyltranspeptidase) x 2 | ||||||
Keywords | TRANSFERASE / gamma-glutamyltransferase / ggt / gamma-gtp | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.95 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 | 2e0x.cif.gz | 220.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e0x.ent.gz | 175.1 KB | Display | PDB format |
PDBx/mmJSON format | 2e0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/2e0x ftp://data.pdbj.org/pub/pdb/validation_reports/e0/2e0x | HTTPS FTP |
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-Related structure data
Related structure data | 2e0wC 2e0yC 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 | #4: 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: 2.6 Å3/Da / Density % sol: 52.65 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 4000, 0.2M calcium chloride, 0.1M Tris-HCl, pH 8.5, 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: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 29, 2006 |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 89113 / Num. obs: 89113 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.095 / Χ2: 0.952 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3 % / Rmerge(I) obs: 0.317 / Num. unique all: 8681 / Χ2: 0.546 / % possible all: 96.4 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A MOLECULE (CHAIN ID A,B) OF THE PDB ENTRY 2DBU Resolution: 1.95→29.91 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.41 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 14.965 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→29.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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