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Yorodumi- PDB-1r4w: Crystal structure of Mitochondrial class kappa glutathione transferase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r4w | ||||||
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Title | Crystal structure of Mitochondrial class kappa glutathione transferase | ||||||
Components | Glutathione S-transferase, mitochondrial | ||||||
Keywords | TRANSFERASE / glutathione-S-transferase / glutathione transferase / kappa GST / rGSTK1-1 | ||||||
Function / homology | Function and homology information Glutathione conjugation / Peroxisomal protein import / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / epithelial cell differentiation / glutathione metabolic process / peroxisome / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR with anomalous Hg / Resolution: 2.5 Å | ||||||
Authors | Ladner, J.E. / Parsons, J.F. / Rife, C.L. / Gilliland, G.L. / Armstrong, R.N. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Parallel Evolutionary Pathways for Glutathione Transferases: Structure and Mechanism of the Mitochondrial Class Kappa Enzyme rGSTK1-1 Authors: Ladner, J.E. / Parsons, J.F. / Rife, C.L. / Gilliland, G.L. / Armstrong, R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r4w.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r4w.ent.gz | 150.1 KB | Display | PDB format |
PDBx/mmJSON format | 1r4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r4w_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1r4w_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 1r4w_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 1r4w_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/1r4w ftp://data.pdbj.org/pub/pdb/validation_reports/r4/1r4w | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25524.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GSGSTK1-1 / Plasmid: pET-20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P24473, glutathione transferase #2: Chemical | ChemComp-GSH / #3: Water | ChemComp-HOH / | Nonpolymer details | HOH 723 MAY BE A PARTIALLY OCCUPIED SULFATE ION. | |
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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: 2.61 Å3/Da / Density % sol: 52.92 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: well: 13-17% (w/v) PEG 2K, 40-80 mM lithium sulfate, 100 mM sodium citrate; drop: 1:1 protein:well, 0.05% beta-octyl-glucopyranoside, 1.5 mM glutathione, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 4.4 / PH range high: 4 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: 14-BM-D / Wavelength: 1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 35795 / Num. obs: 35795 / % possible obs: 98.4 % / Redundancy: 4 % / Biso Wilson estimate: 33.9 Å2 / Rsym value: 0.072 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 5 / % possible all: 88.7 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 115187 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 88.7 % / Mean I/σ(I) obs: 5 |
-Processing
Software |
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Refinement | Method to determine structure: SIR with anomalous Hg / Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Freidel pairs were used in the refinement.
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 30 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |