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- PDB-6ssu: Crystal structure of Human Microsomal Glutathione S-Transferase 2... -

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Basic information

Entry
Database: PDB / ID: 6ssu
TitleCrystal structure of Human Microsomal Glutathione S-Transferase 2 in complex with co-substrate Glutathione
ComponentsMicrosomal glutathione S-transferase 2
KeywordsTRANSFERASE / 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 / : ...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
5-lipoxygenase-activating protein / FLAP/GST2/LTC4S, conserved site / : / FLAP/GST2/LTC4S family signature. / Membrane-associated, eicosanoid/glutathione metabolism (MAPEG) protein / Membrane associated eicosanoid/glutathione metabolism-like domain superfamily / MAPEG family
Similarity search - Domain/homology
GLUTATHIONE / NITRATE ION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Microsomal glutathione S-transferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsThulasingam, M. / Haeggstrom, J.Z.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council10350 Sweden
CitationJournal: 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
DepositionSep 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_radiation_wavelength / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microsomal glutathione S-transferase 2
B: Microsomal glutathione S-transferase 2
C: Microsomal glutathione S-transferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7868
Polymers52,3963
Non-polymers1,3905
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-60 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.280, 152.370, 71.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNASNLYSLYSchain AAA4 - 14210 - 148
2GLYGLYLYSLYSchain BBB3 - 1419 - 147
3ASNASNGLUGLUchain CCC4 - 13310 - 139

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Components

#1: Protein Microsomal glutathione S-transferase 2 / Microsomal GST-2 / Microsomal GST-II


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
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 5.5
Details: 0.1M MES pH 5.5 0.4M Lithium citrate 0.1M Sodium nitrate 20% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.49→46.28 Å / Num. obs: 21514 / % possible obs: 99.79 % / Redundancy: 7.5 % / Biso Wilson estimate: 58.65 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.12
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 2106 / CC1/2: 0.605 / % possible all: 99.25

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Processing

Software
NameVersionClassification
PHENIX1.9_1683refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SSR

6ssr


Resolution: 2.499→46.28 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 1075 5 %
Rwork0.2214 20424 -
obs0.2238 21499 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.18 Å2 / Biso mean: 59.8245 Å2 / Biso min: 32.7 Å2
Refinement stepCycle: final / Resolution: 2.499→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 82 46 3340
Biso mean--72.71 60.92 -
Num. residues----408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013384
X-RAY DIFFRACTIONf_angle_d1.2734583
X-RAY DIFFRACTIONf_chiral_restr0.058509
X-RAY DIFFRACTIONf_plane_restr0.006567
X-RAY DIFFRACTIONf_dihedral_angle_d13.7031169
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1803X-RAY DIFFRACTION8.101TORSIONAL
12B1803X-RAY DIFFRACTION8.101TORSIONAL
13C1803X-RAY DIFFRACTION8.101TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4992-2.61290.38321310.3235249599
2.6129-2.75070.35051330.28252531100
2.7507-2.9230.27471310.25982489100
2.923-3.14860.34021340.25692553100
3.1486-3.46540.29831330.22452534100
3.4654-3.96660.29921360.21012575100
3.9666-4.99660.22181350.1922563100
4.9966-46.280.24371420.21282684100

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