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

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Basic information

Entry
Database: PDB / ID: 6ssr
TitleCrystal structure of Human Microsomal Glutathione S-Transferase 2 at 3.8 Angstroms resolution
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
Microsomal glutathione S-transferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsThulasingam, M. / Nji, E. / Rinaldo-Matthis, A. / 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

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


Theoretical massNumber of molelcules
Total (without water)52,3963
Polymers52,3963
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-60 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.942, 151.149, 70.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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
11LEULEUAA4 - 13710 - 143
21LEULEUBB4 - 13710 - 143
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

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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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 5.5 / Details: 0.1M MES 0.4M Lithium citrate 40% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UUI

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
RfactorNum. reflection% reflectionSelection details
Rfree0.33682 301 5 %RANDOM
Rwork0.305 ---
obs0.3067 5707 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 139.126 Å2
Baniso -1Baniso -2Baniso -3
1--8.78 Å20 Å20 Å2
2---9.22 Å20 Å2
3---18 Å2
Refinement stepCycle: 1 / Resolution: 3.8→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 0 0 3148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023232
X-RAY DIFFRACTIONr_bond_other_d0.0030.023102
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.954393
X-RAY DIFFRACTIONr_angle_other_deg0.93337060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2495398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9322.214131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00615500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.811518
X-RAY DIFFRACTIONr_chiral_restr0.0710.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023649
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02831
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.26813.9711601
X-RAY DIFFRACTIONr_mcbond_other10.26613.971600
X-RAY DIFFRACTIONr_mcangle_it16.7320.9541996
X-RAY DIFFRACTIONr_mcangle_other16.72720.9561997
X-RAY DIFFRACTIONr_scbond_it8.41314.3561631
X-RAY DIFFRACTIONr_scbond_other8.40814.3551629
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.49621.4012397
X-RAY DIFFRACTIONr_long_range_B_refined26.37313739
X-RAY DIFFRACTIONr_long_range_B_other26.37313740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A84760.12
12B84760.12
21A82040.12
22C82040.12
31B82100.13
32C82100.13
LS refinement shellResolution: 3.801→3.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 22 -
Rwork0.427 422 -
obs--99.78 %

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