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- PDB-2dbw: Crystal Structure of Gamma-glutamyltranspeptidase from Escherichi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dbw | ||||||
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Title | Crystal Structure of Gamma-glutamyltranspeptidase from Escherichia coli Acyl-Enzyme Intermediate | ||||||
![]() | (Gamma-glutamyltranspeptidase) x 2 | ||||||
![]() | TRANSFERASE / gamma-glutamyltransferase / ggt / gamma-gtp / glutathione / acyl-enzyme intermediate | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okada, T. / Wada, K. / Fukuyama, K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.4 KB | Display | ![]() |
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PDB format | ![]() | 188.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.2 KB | Display | ![]() |
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Full document | ![]() | 491.7 KB | Display | |
Data in XML | ![]() | 49.7 KB | Display | |
Data in CIF | ![]() | 73 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dbuSC ![]() 2dbxC ![]() 2dg5C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 20262.951 Da / Num. of mol.: 2 / Fragment: SMALL SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 12.5% PEG 4000, 0.2M magnesium sulfate, 5% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2005 |
Radiation | Monochromator: SI(111) DOUBLE MONOCHROMATER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 120057 / Num. obs: 120057 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 8 % / Rmerge(I) obs: 0.348 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DBU Resolution: 1.8→46.42 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2686055.04 / 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: 46.016 Å2 / ksol: 0.36887 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→46.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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