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Yorodumi- PDB-6ssr: Crystal structure of Human Microsomal Glutathione S-Transferase 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ssr | ||||||
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Title | Crystal structure of Human Microsomal Glutathione S-Transferase 2 at 3.8 Angstroms resolution | ||||||
Components | Microsomal glutathione S-transferase 2 | ||||||
Keywords | TRANSFERASE / ER MEMBRANE PROTEIN / GLUTATHIONE TRANSFERASE / MAPEG / MGST2 / INTEGRAL MEMBRANE ENZYME | ||||||
Function / homology | Function and homology information membrane lipid catabolic process / leukotriene-C4 synthase / leukotriene-C4 synthase activity / glutathione biosynthetic process / Aflatoxin activation and detoxification / glutathione binding / Glutathione conjugation / leukotriene biosynthetic process / glutathione peroxidase activity / glutathione transferase ...membrane lipid catabolic process / leukotriene-C4 synthase / leukotriene-C4 synthase activity / glutathione biosynthetic process / Aflatoxin activation and detoxification / glutathione binding / Glutathione conjugation / leukotriene biosynthetic process / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / enzyme activator activity / : / lipid metabolic process / positive regulation of inflammatory response / nuclear envelope / response to lipopolysaccharide / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Thulasingam, M. / Nji, E. / Rinaldo-Matthis, A. / Haeggstrom, J.Z. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Crystal structures of human MGST2 reveal synchronized conformational changes regulating catalysis. Authors: Thulasingam, M. / Orellana, L. / Nji, E. / Ahmad, S. / Rinaldo-Matthis, A. / Haeggstrom, J.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ssr.cif.gz | 90.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ssr.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ssr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ssr_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 6ssr_full_validation.pdf.gz | 453.8 KB | Display | |
Data in XML | 6ssr_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 6ssr_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/6ssr ftp://data.pdbj.org/pub/pdb/validation_reports/ss/6ssr | HTTPS FTP |
-Related structure data
Related structure data | 6sssC 6ssuC 6sswC 2uuiS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 17465.410 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGST2, GST2 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q99735, glutathione transferase |
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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: 2.77 Å3/Da / Density % sol: 55.62 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / pH: 5.5 / Details: 0.1M MES 0.4M Lithium citrate 40% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→44.45 Å / Num. obs: 6009 / % possible obs: 99.42 % / Redundancy: 12.2 % / CC1/2: 0.987 / Rmerge(I) obs: 0.423 / Net I/σ(I): 4.64 |
Reflection shell | Resolution: 3.8→3.93 Å / Redundancy: 12.4 % / Rmerge(I) obs: 2.247 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 6009 / CC1/2: 0.663 / % possible all: 99.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2UUI Resolution: 3.8→44.45 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.915 / SU B: 89.593 / SU ML: 1.09 / Cross valid method: THROUGHOUT / ESU R Free: 0.969 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 139.126 Å2
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Refinement step | Cycle: 1 / Resolution: 3.8→44.45 Å
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Refine LS restraints |
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