+Open data
-Basic information
Entry | Database: PDB / ID: 1m0t | ||||||
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Title | Yeast Glutathione Synthase | ||||||
Components | glutathione synthetase | ||||||
Keywords | LIGASE / AMINE/CARBOXYLATE LIGASE / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information Glutathione synthesis and recycling / glutathione synthase / glutathione synthase activity / glutathione biosynthetic process / glutathione binding / magnesium ion binding / protein homodimerization activity / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Gogos, A. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Structure / Year: 2002 Title: Large Conformational Changes in the Catalytic Cycle of Glutathione Synthase Authors: Gogos, A. / Shapiro, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m0t.cif.gz | 207.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m0t.ent.gz | 164.5 KB | Display | PDB format |
PDBx/mmJSON format | 1m0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/1m0t ftp://data.pdbj.org/pub/pdb/validation_reports/m0/1m0t | HTTPS FTP |
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-Related structure data
Related structure data | 1m0wC 2hgsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 55878.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: GSH2 / Plasmid: pET28TEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q08220, glutathione synthase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.72 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium sulphate, PEG 400, Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2001 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 45753 / Num. obs: 45753 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 10.1 / Num. unique all: 4570 / Rsym value: 0.177 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 573251 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HGS Resolution: 2.3→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 84.6575 Å2 / ksol: 0.442753 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. reflection Rfree: 2340 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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