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

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Basic information

Entry
Database: PDB / ID: 6sss
TitleCrystal structure of Human Microsomal Glutathione S-Transferase 2
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 / glutathione binding / Aflatoxin activation and detoxification / Glutathione conjugation / glutathione peroxidase activity / leukotriene biosynthetic process / glutathione transferase ...membrane lipid catabolic process / leukotriene-C4 synthase / leukotriene-C4 synthase activity / glutathione biosynthetic process / glutathione binding / Aflatoxin activation and detoxification / Glutathione conjugation / glutathione peroxidase activity / leukotriene biosynthetic process / 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
: / 1-(8Z-hexadecenoyl)-sn-glycerol / THIOCYANATE ION / Microsomal glutathione S-transferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å
AuthorsThulasingam, M. / Nji, E. / 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 2.0Apr 7, 2021Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / 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 3.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / struct_ncs_dom_lim
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _pdbx_entity_nonpoly.name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_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_auth_seq_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
Revision 3.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
D: Microsomal glutathione S-transferase 2
E: Microsomal glutathione S-transferase 2
F: Microsomal glutathione S-transferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,40826
Polymers104,7926
Non-polymers2,61520
Water1,27971
1
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)54,13613
Polymers52,3963
Non-polymers1,74010
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-143 kcal/mol
Surface area17340 Å2
MethodPISA
2
D: Microsomal glutathione S-transferase 2
E: Microsomal glutathione S-transferase 2
F: Microsomal glutathione S-transferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,27113
Polymers52,3963
Non-polymers87510
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-157 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.886, 72.162, 72.692
Angle α, β, γ (deg.)67.930, 86.710, 86.860
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid
31chain C and segid
41chain D and segid
51chain E and segid
61chain F and segid

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 4 - 131 / Label seq-ID: 10 - 137

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and segidAA
2chain B and segidBB
3chain C and segidCC
4chain D and segidDD
5chain E and segidEE
6chain F and segidFF

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 17465.410 Da / Num. of mol.: 6
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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Non-polymers , 7 types, 91 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-M88 / 1-(8Z-hexadecenoyl)-sn-glycerol / 2,3-dihydroxypropyl (Z)-hexadec-8-enoate / [(2S)-2,3-bis(oxidanyl)propyl] (Z)-hexadec-8-enoate


Mass: 328.487 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C19H36O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 4.5
Details: 0.1M Sodium acetate pH 4.5 0.4M Sodium sulfate 0.1M Potassium thiocyanate 17% 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: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.49→43.329 Å / Num. obs: 35150 / % possible obs: 98.29 % / Redundancy: 3.5 % / CC1/2: 0.989 / Net I/σ(I): 5.31
Reflection shellResolution: 2.49→2.58 Å / Mean I/σ(I) obs: 0.99 / Num. unique obs: 35150 / CC1/2: 0.433

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Processing

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

6ssr


Resolution: 2.498→43.329 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 29.99
RfactorNum. reflection% reflection
Rfree0.267 1755 5 %
Rwork0.2184 --
obs0.2209 35132 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.66 Å2 / Biso mean: 54.355 Å2 / Biso min: 24.04 Å2
Refinement stepCycle: final / Resolution: 2.498→43.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6176 0 235 71 6482
Biso mean--56.76 49.96 -
Num. residues----786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056485
X-RAY DIFFRACTIONf_angle_d0.888798
X-RAY DIFFRACTIONf_chiral_restr0.034977
X-RAY DIFFRACTIONf_plane_restr0.0041077
X-RAY DIFFRACTIONf_dihedral_angle_d14.1352232
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4746X-RAY DIFFRACTION10.228TORSIONAL
12B4746X-RAY DIFFRACTION10.228TORSIONAL
13C4746X-RAY DIFFRACTION10.228TORSIONAL
14D4746X-RAY DIFFRACTION10.228TORSIONAL
15E4746X-RAY DIFFRACTION10.228TORSIONAL
16F4746X-RAY DIFFRACTION10.228TORSIONAL
LS refinement shell

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

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.498-2.56510.3521310.3054248196
2.5651-2.64060.34581340.3013255398
2.6406-2.72580.37381360.2839259098
2.7258-2.82320.31981350.2685256099
2.8232-2.93620.2721370.252259298
2.9362-3.06980.2911340.2433256098
3.0698-3.23160.30761370.2296259698
3.2316-3.4340.27651360.2166258299
3.434-3.6990.27381330.2227254398
3.699-4.0710.23531340.2018256498
4.071-4.65950.23731370.1751260299
4.6595-5.86820.25421350.2044257399
5.86820.21231360.1911258199
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)
10.0459-0.2328-0.36180.31980.37330.4589-0.0134-0.22710.06470.19150.14290.3368-0.2487-0.1972-00.3219-0.0760.00060.3527-0.00210.362712.952923.2347-8.4399
21.65581.5477-0.45561.77740.04390.6806-0.2077-0.3685-0.77340.7858-0.2522-1.04280.61620.29590.02050.6313-0.0334-0.02410.40390.14590.395116.76412.493-2.6108
30.5345-0.0299-0.13880.16130.0190.55970.02150.016-0.0247-0.0462-0.1105-0.04010.0562-0.086600.2908-0.04070.02210.3095-0.00510.33396.033320.6939-14.4967
40.9857-0.33530.55620.92620.51960.7008-0.11940.13730.2135-0.23780.44690.3165-0.0591-0.739500.3276-0.0795-0.04560.3441-0.01630.34130.603725.9806-27.0309
50.5868-0.3526-0.19770.57450.62770.5609-0.14660.01760.0048-0.22880.33770.30860.195-0.1232-0.00020.2838-0.05070.03050.38830.00340.44066.522915.623-28.8351
61.4104-0.59330.2770.52450.10720.31940.00060.0739-0.10130.17240.14290.0008-0.0602-0.10220.00010.3081-0.01140.01010.32240.02120.273813.512210.3762-24.3473
70.6611-0.19980.04580.30740.11040.8395-0.01680.1955-0.1124-0.30740.2043-0.06060.0427-0.0008-00.3376-0.00620.02460.3795-0.01150.357220.858515.7814-35.3165
80.81270.1842-0.59010.25430.13990.5811-0.0138-0.0958-0.0332-0.3672-0.1798-0.41610.230.279700.44940.0619-0.01050.37880.01040.430126.94210.7655-22.3507
91.0852-0.20940.11860.46560.23271.08630.1065-0.2998-0.05780.13610.0062-0.11390.0010.21100.3610.0416-0.03440.4094-0.03970.384124.918222.5702-12.3956
100.5943-0.48090.35180.27580.00910.4054-0.1215-0.0293-0.0414-0.65570.3404-0.0137-0.06230.2594-0.00040.4921-0.00880.03580.44580.02390.403755.75527.3457-54.8601
110.55090.20.23840.51150.34460.52380.04960.2660.0337-0.2493-0.0189-0.173-0.03270.1496-0.00010.41050.02250.05490.3554-0.00630.350252.620224.6294-65.4085
120.06960.36940.4580.58170.55290.62910.2160.7030.04310.20750.20060.54720.0153-0.09190.00610.44660.0477-0.00620.44460.01360.43940.243720.2837-69.9019
130.2008-0.2291-0.58140.49291.09162.4404-0.25730.08810.5336-1.06390.41560.1156-0.71980.28970.14410.70420.0714-0.0450.48210.08920.620743.899141.0629-75.5215
140.71180.1528-0.51410.57650.08630.55390.0310.1194-0.0399-0.2873-0.20610.13740.1196-0.1244-0.00020.3487-0.023-0.08960.3496-0.00190.359233.375722.8268-63.6851
151.03470.2589-0.25950.32530.37980.6021-0.2614-0.04180.00010.20410.45250.352-0.1031-0.7924-0.00120.40750.08460.02710.48990.0430.406327.112419.4349-54.5259
161.17710.9727-0.08661.12020.72571.206-0.00180.3320.0480.18-0.2351-0.1756-0.02720.17380.00010.3102-0.0089-0.04250.3404-0.02060.287333.912327.6717-49.4048
170.86620.40090.23340.21990.08340.51010.14110.05220.0967-0.14520.01210.36740.0702-0.122300.32980.01040.02040.3337-0.00890.328940.784633.2367-53.8855
180.2073-0.10510.24060.0726-0.05290.1378-0.0228-0.64710.2032-0.01910.1629-0.0111-0.0341-0.3201-0.00010.335-0.0029-0.01650.3852-0.03020.399542.43929.7461-41.8167
190.55020.35840.24880.12030.18430.8805-0.05870.14860.40290.39180.0713-0.7352-0.07040.0955-0.00060.2554-0.01670.02750.33880.03850.346353.2826.5683-43.7537
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 32 )A3 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 43 )A33 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 100 )A44 - 100
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 138 )A101 - 138
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 32 )B4 - 32
6X-RAY DIFFRACTION6chain 'B' and (resid 33 through 73 )B33 - 73
7X-RAY DIFFRACTION7chain 'B' and (resid 74 through 133 )B74 - 133
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 43 )C3 - 43
9X-RAY DIFFRACTION9chain 'C' and (resid 44 through 135 )C44 - 135
10X-RAY DIFFRACTION10chain 'D' and (resid 4 through 32 )D4 - 32
11X-RAY DIFFRACTION11chain 'D' and (resid 33 through 131 )D33 - 131
12X-RAY DIFFRACTION12chain 'E' and (resid 4 through 32 )E4 - 32
13X-RAY DIFFRACTION13chain 'E' and (resid 33 through 43 )E33 - 43
14X-RAY DIFFRACTION14chain 'E' and (resid 44 through 100 )E44 - 100
15X-RAY DIFFRACTION15chain 'E' and (resid 101 through 133 )E101 - 133
16X-RAY DIFFRACTION16chain 'F' and (resid 4 through 32 )F4 - 32
17X-RAY DIFFRACTION17chain 'F' and (resid 33 through 73 )F33 - 73
18X-RAY DIFFRACTION18chain 'F' and (resid 74 through 100 )F74 - 100
19X-RAY DIFFRACTION19chain 'F' and (resid 101 through 132 )F101 - 132

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