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Yorodumi- PDB-1va6: Crystal structure of Gamma-glutamylcysteine synthetase from Esche... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1va6 | ||||||
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Title | Crystal structure of Gamma-glutamylcysteine synthetase from Escherichia Coli B complexed with Transition-state analogue | ||||||
Components | Glutamate--cysteine ligase | ||||||
Keywords | LIGASE / Glutathione homeostasis / Beta barrel / Peptide synthesis / Transition state analogue | ||||||
Function / homology | Function and homology information glutamate-cysteine ligase / glutamate-cysteine ligase activity / cellular response to mercury ion / glutathione biosynthetic process / cellular response to arsenic-containing substance / hyperosmotic response / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Hibi, T. / Nii, H. / Nakatsu, T. / Kato, H. / Hiratake, J. / Oda, J. | ||||||
Citation | Journal: PROC.NATL.ACAD.SCI.USA / Year: 2004 Title: Crystal structure of gamma-glutamylcysteine synthetase: insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis Authors: Hibi, T. / Nii, H. / Nakatsu, T. / Kimura, A. / Kato, H. / Hiratake, J. / Oda, J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Escherichia coli B gamma-glutamylcysteine synthetase: modification, purification, crystallization and preliminary crystallographic analysis Authors: Hibi, T. / Hisada, H. / Nakatsu, T. / Kato, H. / Oda, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1va6.cif.gz | 225.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1va6.ent.gz | 177.2 KB | Display | PDB format |
PDBx/mmJSON format | 1va6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/1va6 ftp://data.pdbj.org/pub/pdb/validation_reports/va/1va6 | HTTPS FTP |
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-Related structure data
Related structure data | 1v4gSC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 58268.844 Da / Num. of mol.: 2 / Mutation: C106S, C164S, C205S, C223S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GSH-I / Plasmid: pKGC20 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A6W9, glutamate-cysteine ligase |
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-Non-polymers , 5 types, 360 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.78 Å3/Da / Density % sol: 55.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 2000MME, MgCl2, Tris-HCl buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 2, 2003 |
Radiation | Monochromator: ROTATED-INCLINED DOUBLE-CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.8 Å / Num. all: 73644 / Num. obs: 73622 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.5 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V4G Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.608 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.169 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.31 Å2
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Refine analyze | Luzzati coordinate error obs: 0.319 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20 /
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