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Yorodumi- PDB-1v4g: Crystal Structure of gamma-Glutamylcysteine Synthetase from Esche... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v4g | ||||||
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Title | Crystal Structure of gamma-Glutamylcysteine Synthetase from Escherichia coli B | ||||||
Components | Glutamate--cysteine ligase | ||||||
Keywords | LIGASE / glutathione regulation / beta barrel / peptide synthesis | ||||||
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 / MAD / Resolution: 2.5 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 | 1v4g.cif.gz | 396.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v4g.ent.gz | 326.1 KB | Display | PDB format |
PDBx/mmJSON format | 1v4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v4g_validation.pdf.gz | 465.3 KB | Display | wwPDB validaton report |
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Full document | 1v4g_full_validation.pdf.gz | 502.2 KB | Display | |
Data in XML | 1v4g_validation.xml.gz | 73.6 KB | Display | |
Data in CIF | 1v4g_validation.cif.gz | 101.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/1v4g ftp://data.pdbj.org/pub/pdb/validation_reports/v4/1v4g | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 58296.859 Da / Num. of mol.: 4 / Mutation: C106S, C164S, C205S, C232S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GSH-I / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A6W9, glutamate-cysteine ligase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.74 Å3/Da / Density % sol: 73.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: sodium formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.5→48.7 Å / Num. all: 144157 / Num. obs: 144157 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 9 | ||||||||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.4 / Num. unique all: 14422 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.407 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 32.97 Å2
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Refine analyze | Luzzati coordinate error obs: 0.385 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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