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- PDB-5b5t: Crystal Structure of Escherichia coli Gamma-Glutamyltranspeptidas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b5t | ||||||
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Title | Crystal Structure of Escherichia coli Gamma-Glutamyltranspeptidase in Complex with peptidyl phosphonate inhibitor 1b | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / glutathione / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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. / Fukuyama, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Phosphonate-based irreversible inhibitors of human gamma-glutamyl transpeptidase (GGT). GGsTop is a non-toxic and highly selective inhibitor with critical electrostatic interaction with an ...Title: Phosphonate-based irreversible inhibitors of human gamma-glutamyl transpeptidase (GGT). GGsTop is a non-toxic and highly selective inhibitor with critical electrostatic interaction with an active-site residue Lys562 for enhanced inhibitory activity Authors: Kamiyama, A. / Nakajima, M. / Han, L. / Wada, K. / Mizutani, M. / Tabuchi, Y. / Kojima-Yuasa, A. / Matsui-Yuasa, I. / Suzuki, H. / Fukuyama, K. / Watanabe, B. / Hiratake, J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.5 KB | Display | ![]() |
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PDB format | ![]() | 192.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 52.5 KB | Display | |
Data in CIF | ![]() | 80.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dbuS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: ggt, b3447, JW3412 / Production host: ![]() ![]() References: UniProt: P18956, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase #2: Protein | Mass: 20028.475 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: ggt, b3447, JW3412 / Production host: ![]() ![]() References: UniProt: P18956, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase #3: Chemical | #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: 54.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting 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: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 26, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 135141 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.56 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DBU Resolution: 1.7→37.329 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→37.329 Å
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Refine LS restraints |
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LS refinement shell |
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