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- PDB-4gg2: The crystal structure of glutamate-bound human gamma-glutamyltran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gg2 | ||||||
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Title | The crystal structure of glutamate-bound human gamma-glutamyltranspeptidase 1 | ||||||
![]() | (Gamma-glutamyltranspeptidase 1 ...) x 2 | ||||||
![]() | HYDROLASE / NTN-HYDROLYASE / GLUTATHIONINE METABOLISM / N-GLYCOSYLATION / EXTERIOR CELL SURFACE | ||||||
Function / homology | ![]() leukotriene-C4 hydrolase / peptidyltransferase activity / leukotriene-C(4) hydrolase / leukotriene D4 biosynthetic process / Defective GGT1 causes GLUTH / Defective GGT1 in aflatoxin detoxification causes GLUTH / LTC4-CYSLTR mediated IL4 production / Glutathione synthesis and recycling / peptide modification / gamma-glutamyltransferase ...leukotriene-C4 hydrolase / peptidyltransferase activity / leukotriene-C(4) hydrolase / leukotriene D4 biosynthetic process / Defective GGT1 causes GLUTH / Defective GGT1 in aflatoxin detoxification causes GLUTH / LTC4-CYSLTR mediated IL4 production / Glutathione synthesis and recycling / peptide modification / gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / leukotriene metabolic process / glutamate metabolic process / glutathione biosynthetic process / Aflatoxin activation and detoxification / cysteine biosynthetic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of immune system process / Paracetamol ADME / amino acid metabolic process / zymogen activation / fatty acid metabolic process / regulation of inflammatory response / spermatogenesis / proteolysis / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | West, M.B. / Chen, Y. / Wickham, S. / Heroux, A. / Cahill, K. / Hanigan, M.H. / Mooers, B.H.M. | ||||||
![]() | ![]() Title: Novel Insights into Eukaryotic gamma-Glutamyltranspeptidase 1 from the Crystal Structure of the Glutamate-bound Human Enzyme. Authors: West, M.B. / Chen, Y. / Wickham, S. / Heroux, A. / Cahill, K. / Hanigan, M.H. / Mooers, B.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.1 KB | Display | ![]() |
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PDB format | ![]() | 172.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.3 KB | Display | ![]() |
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Full document | ![]() | 476.4 KB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 38.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gdxSC 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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Unit cell |
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Components
-Gamma-glutamyltranspeptidase 1 ... , 2 types, 2 molecules AB
#1: Protein | Mass: 38561.715 Da / Num. of mol.: 1 / Fragment: unp residues 28-380 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P19440, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase, leukotriene-C4 hydrolase |
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#2: Protein | Mass: 20014.438 Da / Num. of mol.: 1 / Fragment: unp residues 381-569 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P19440, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase, leukotriene-C4 hydrolase |
-Sugars , 1 types, 6 molecules ![](data/chem/img/NAG.gif)
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 384 molecules ![](data/chem/img/IOD.gif)
![](data/chem/img/GLU.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GLU.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-IOD / #5: Chemical | ChemComp-GLU / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 15-25% PEG3350, 100 mM Ammonium chloride, 0.5 mM L-glutamate, 100 mM Na:Cacodylate pH 6.0 , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2011 |
Radiation | Monochromator: Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.18 Å / Num. all: 35539 / Num. obs: 34317 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 18.5 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 31.3 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.563 / % possible all: 75.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 4GDX Resolution: 2.21→43.975 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 18.22 / Stereochemistry target values: ML Details: Used Bijvoet pairs in refinement. The statistics above are for the merged reflections.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→43.975 Å
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Refine LS restraints |
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LS refinement shell |
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