[English] 日本語
Yorodumi- PDB-2gwc: Crystal structure of plant glutamate cysteine ligase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gwc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of plant glutamate cysteine ligase in complex with a transition state analogue | |||||||||
Components | Glutamate cysteine ligase | |||||||||
Keywords | LIGASE / disulfide bridges / glutathione biosynthesis / beta-hairpin / redox regulation | |||||||||
Function / homology | Function and homology information oxoacid metabolic process / glutamate-cysteine ligase / glutamate-cysteine ligase activity / glutathione biosynthetic process / chloroplast / ATP binding Similarity search - Function | |||||||||
Biological species | Brassica juncea (brown mustard) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.18 Å | |||||||||
Authors | Hothorn, M. / Wachter, A. / Gromes, R. / Stuwe, T. / Rausch, T. / Scheffzek, K. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural basis for the redox control of plant glutamate cysteine ligase. Authors: Hothorn, M. / Wachter, A. / Gromes, R. / Stuwe, T. / Rausch, T. / Scheffzek, K. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2gwc.cif.gz | 694.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2gwc.ent.gz | 598.2 KB | Display | PDB format |
PDBx/mmJSON format | 2gwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gwc_validation.pdf.gz | 514.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2gwc_full_validation.pdf.gz | 548.1 KB | Display | |
Data in XML | 2gwc_validation.xml.gz | 123.7 KB | Display | |
Data in CIF | 2gwc_validation.cif.gz | 175.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/2gwc ftp://data.pdbj.org/pub/pdb/validation_reports/gw/2gwc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: PRO / End label comp-ID: TYR / Refine code: 2 / Auth seq-ID: 80 - 514 / Label seq-ID: 15 - 449
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | The oxidized state of the enzyme is associated with a dimeric configuration. The asymmetric unit contains four dimers (A-B, C-D, E-F, G-H) |
-Components
#1: Protein | Mass: 51818.281 Da / Num. of mol.: 8 / Fragment: glutamate cysteine ligase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brassica juncea (brown mustard) / Gene: GSH1 / Plasmid: pETM20 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami (DE3) / References: UniProt: O23736, glutamate-cysteine ligase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-BSC / ( #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.6 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15% PEG 3350, 0.2 M magnesium acetate tetrahydrate, 0.1 M tricine, 0.01 M L-buthionine(S,R)sulfoximine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9797, 0.9778, 0,.9737 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 18, 2005 | |||||||||||||||
Radiation | Monochromator: transparent diamond monochromators / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 2.18→99.5 Å / Num. obs: 197271 / % possible obs: 95.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.104 / Net I/σ(I): 13.6 | |||||||||||||||
Reflection shell | Resolution: 2.18→2.27 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 40871 / Rsym value: 0.457 / % possible all: 89.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.18→99.5 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.676 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.283 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.442 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→99.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
|