[English] 日本語
![](img/lk-miru.gif)
- PDB-2z8j: Crystal Structure of Escherichia coli gamma-Glutamyltranspeptidas... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2z8j | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Escherichia coli gamma-Glutamyltranspeptidase in Complex with Azaserine prepared in the dark | ||||||
![]() | (Gamma-glutamyltranspeptidase) x 2 | ||||||
![]() | TRANSFERASE / Azaserine with a diazo group / covalent bond with Thr391 / Acyltransferase / Glutathione biosynthesis / Zymogen | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Wada, K. / Irie, M. / Fukuyama, K. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 221.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 175.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 506.3 KB | Display | |
Data in XML | ![]() | 47.1 KB | Display | |
Data in CIF | ![]() | 66 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2z8iC ![]() 2z8kC ![]() 2dbuS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 20028.475 Da / Num. of mol.: 2 / Fragment: small chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.86 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 78471 / Num. obs: 78471 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.331 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2DBU Resolution: 2.05→40.14 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 78582.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.2703 Å2 / ksol: 0.370642 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→40.14 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|