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

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Basic information

Entry
Database: PDB / ID: 6ssw
TitleCrystal structure of Human Microsomal Glutathione S-Transferase 2 in complex with an Inhibitor Glutathione sulfonic acid
ComponentsMicrosomal glutathione S-transferase 2
KeywordsTRANSFERASE / INTEGRAL MEMBRANE PROTEIN / GLUTATHIONE TRANSFERASE / MAPEG / MGST2
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 SULFONIC ACID / Microsomal glutathione S-transferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 / Refinement description
Category: citation / citation_author ...citation / citation_author / diffrn_radiation_wavelength / diffrn_source / pdbx_refine_tls_group
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

Downloads & links

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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)53,4626
Polymers52,3963
Non-polymers1,0663
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-64 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.420, 148.870, 70.330
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
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA4 - 13810 - 144
21ASNASNBB4 - 13810 - 144
12ASPASPAA4 - 13210 - 138
22ASPASPCC4 - 13210 - 138
13ASPASPBB4 - 13210 - 138
23ASPASPCC4 - 13210 - 138

NCS ensembles :
ID
1
2
3

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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-GTS / GLUTATHIONE SULFONIC ACID


Mass: 355.322 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N3O9S / Feature type: SUBJECT OF INVESTIGATION
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: 3.16 Å3/Da / Density % sol: 61.11 %
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 malonate 20% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.99→45.26 Å / Num. obs: 11946 / % possible obs: 99.72 % / Redundancy: 9.1 % / CC1/2: 0.998 / Net I/σ(I): 9.36
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 1.11 / Num. unique obs: 11946 / CC1/2: 0.678 / % possible all: 99.23

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SSR

6ssr


Resolution: 3→45.26 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.905 / SU B: 78.836 / SU ML: 0.545 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.464
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2834 598 5 %RANDOM
Rwork0.2432 ---
obs0.2452 11347 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 170.01 Å2 / Biso mean: 84.483 Å2 / Biso min: 67.89 Å2
Baniso -1Baniso -2Baniso -3
1-7.35 Å20 Å20 Å2
2---6.64 Å20 Å2
3----0.71 Å2
Refinement stepCycle: final / Resolution: 3→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3197 0 69 0 3266
Biso mean--100.87 --
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123348
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173145
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.6314548
X-RAY DIFFRACTIONr_angle_other_deg1.4081.5627216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4215403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57320.382157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88815515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2611518
X-RAY DIFFRACTIONr_chiral_restr0.0740.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023717
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02797
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A44040.1
12B44040.1
21A42720.1
22C42720.1
31B42580.11
32C42580.11
LS refinement shellResolution: 3→3.076 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.369 43 -
Rwork0.505 807 -
obs--98.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3828-0.65140.1694.2749-2.80782.9026-0.2010.16680.02090.10580.1164-0.032-0.0987-0.22210.08470.9278-0.04090.00660.2861-0.06890.0212115.7396172.9189-2.9112
22.28470.69730.65265.96420.93311.5113-0.0906-0.01590.0847-0.00230.2277-0.8284-0.10560.2088-0.13710.8985-0.02220.09830.39580.03060.1595135.3639174.8447-3.659
32.5461-1.184-0.6216.0992-0.34891.6903-0.1943-0.1957-0.0670.47330.1422-0.0342-0.1811-0.12840.05210.9767-0.123-0.09980.3609-0.05180.0392126.863175.197513.3189
40.47770.22031.41633.5955-0.9164.9186-0.0191-0.1477-0.08530.34840.1834-0.2201-0.2138-0.6581-0.16430.7742-0.0170.11410.8363-0.07740.4911126.417163.38233.5706
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 139
2X-RAY DIFFRACTION2B3 - 142
3X-RAY DIFFRACTION3C4 - 133
4X-RAY DIFFRACTION4A201
5X-RAY DIFFRACTION4B201
6X-RAY DIFFRACTION4C201

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