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Yorodumi- PDB-2z8i: Crystal Structure of Escherichia coli Gamma-Glutamyltranspeptidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z8i | ||||||
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Title | Crystal Structure of Escherichia coli Gamma-Glutamyltranspeptidase in Complex with Azaserine | ||||||
Components | (Gamma-glutamyltranspeptidase) x 2 | ||||||
Keywords | TRANSFERASE / Thr391 formed a covalent bond with azaserine / Acyltransferase / Glutathione biosynthesis / Zymogen | ||||||
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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Wada, K. / Irie, M. / Fukuyama, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal structures of Escherichia coli gamma-glutamyltranspeptidase in complex with azaserine and acivicin: novel mechanistic implication for inhibition by glutamine antagonists Authors: Wada, K. / Hiratake, J. / Irie, M. / Okada, T. / Yamada, C. / Kumagai, H. / Suzuki, 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 | 2z8i.cif.gz | 219.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z8i.ent.gz | 173.1 KB | Display | PDB format |
PDBx/mmJSON format | 2z8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/2z8i ftp://data.pdbj.org/pub/pdb/validation_reports/z8/2z8i | HTTPS FTP |
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-Related structure data
Related structure data | 2z8jC 2z8kC 2dbuS C: citing same article (ref.) S: Starting model for refinement |
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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: 39311.230 Da / Num. of mol.: 2 / Fragment: large chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Plasmid: pSH253 / Production host: Escherichia coli (E. coli) / References: UniProt: P18956, gamma-glutamyltransferase #2: Protein | Mass: 20028.475 Da / Num. of mol.: 2 / Fragment: small chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Plasmid: pSH253 / Production host: Escherichia coli (E. coli) / References: UniProt: P18956, gamma-glutamyltransferase #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 12.5-17.5% PEG 4000, 0.2M CaCl2, 0.1M Tris-HCl, pH 8.4, 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 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 147754 / Num. obs: 147754 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.312 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DBU Resolution: 1.65→29.41 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 183527.77 / 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: 37.1222 Å2 / ksol: 0.390495 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→29.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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