[English] 日本語
Yorodumi- PDB-6zj9: Crystal structure of Equus ferus caballus glutathione transferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zj9 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Equus ferus caballus glutathione transferase A3-3 in complex with glutathione | ||||||||||||
Components | Glutathione S-transferase | ||||||||||||
Keywords | TRANSFERASE / steroid isomerase / detoxication / hormone biosynthesis | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Equus caballus (horse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||||||||
Authors | Skerlova, J. / Ismail, A. / Lindstrom, H. / Sjodin, B. / Mannervik, B. / Stenmark, P. | ||||||||||||
Funding support | Sweden, European Union, 3items
| ||||||||||||
Citation | Journal: Environ Pollut / Year: 2021 Title: Structural and functional analysis of the inhibition of equine glutathione transferase A3-3 by organotin endocrine disrupting pollutants. Authors: Skerlova, J. / Ismail, A. / Lindstrom, H. / Sjodin, B. / Mannervik, B. / Stenmark, P. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6zj9.cif.gz | 62 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6zj9.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 6zj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/6zj9 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/6zj9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6zjcC 1tdiS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 25363.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: GSTA3 / Production host: Escherichia coli (E. coli) / References: UniProt: M9ZT87, glutathione transferase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-GSH / | ||||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.43 % / Description: thin plates |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Bicine/Trizma base pH 8.5, 10% w/v PEG 20 000, 20% v/v PEG MME 550, and 0.02 M of each alcohol (1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, and 1,3-propanediol) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 5, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→99.15 Å / Num. obs: 13931 / % possible obs: 99.9 % / Redundancy: 8.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.058 / Rrim(I) all: 0.176 / Net I/σ(I): 7.5 / Num. measured all: 115753 / Scaling rejects: 81 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1tdi Resolution: 2.2→49.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.2187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.91 Å2 / Biso mean: 31.679 Å2 / Biso min: 10.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→49.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.201→2.258 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|