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Yorodumi- PDB-5lkd: Crystal structure of the Xi glutathione transferase ECM4 from Sac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lkd | ||||||
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Title | Crystal structure of the Xi glutathione transferase ECM4 from Saccharomyces cerevisiae in complex with glutathione | ||||||
Components | Glutathione S-transferase omega-like 2 | ||||||
Keywords | TRANSFERASE / Saccharomyces cerevisiae / glutathione transferase / glutathione / quinone / ECM4 / YKR076W / Glutathionyl-hydroquinone reductase | ||||||
Function / homology | Function and homology information glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cell wall organization / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Schwartz, M. / Didierjean, C. / Hecker, A. / Girardet, J.M. / Morel-Rouhier, M. / Gelhaye, E. / Favier, F. | ||||||
Citation | Journal: Plos One / Year: 2016 Title: Crystal Structure of Saccharomyces cerevisiae ECM4, a Xi-Class Glutathione Transferase that Reacts with Glutathionyl-(hydro)quinones. Authors: Schwartz, M. / Didierjean, C. / Hecker, A. / Girardet, J.M. / Morel-Rouhier, M. / Gelhaye, E. / Favier, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lkd.cif.gz | 287.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lkd.ent.gz | 234.4 KB | Display | PDB format |
PDBx/mmJSON format | 5lkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lkd_validation.pdf.gz | 917 KB | Display | wwPDB validaton report |
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Full document | 5lkd_full_validation.pdf.gz | 918.3 KB | Display | |
Data in XML | 5lkd_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 5lkd_validation.cif.gz | 49.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/5lkd ftp://data.pdbj.org/pub/pdb/validation_reports/lk/5lkd | HTTPS FTP |
-Related structure data
Related structure data | 5lkbC 3ppuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44406.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: ECM4, GTO2, YKR076W / Production host: Escherichia coli (E. coli) References: UniProt: P36156, glutathione transferase, glutathione dehydrogenase (ascorbate) #2: Chemical | #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: 2.06 Å3/Da / Density % sol: 40.42 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / Details: 20% (w/v) PEG 2000 MME, 0.1 M Tris pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979767 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979767 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→47.59 Å / Num. obs: 78066 / % possible obs: 95 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.68→1.72 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.76 / % possible all: 74.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PPU Resolution: 1.68→47.582 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→47.582 Å
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Refine LS restraints |
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LS refinement shell |
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