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- PDB-2gtu: LIGAND-FREE HUMAN GLUTATHIONE S-TRANSFERASE M2-2 (E.C.2.5.1.18), ... -

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Basic information

Entry
Database: PDB / ID: 2gtu
TitleLIGAND-FREE HUMAN GLUTATHIONE S-TRANSFERASE M2-2 (E.C.2.5.1.18), MONOCLINIC CRYSTAL FORM
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / GLUTATHIONE / CONJUGATION / DETOXIFICATION / CYTOSOLIC / DIMER
Function / homology
Function and homology information


nitrobenzene metabolic process / cellular detoxification of nitrogen compound / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / glutathione binding / hepoxilin biosynthetic process / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / relaxation of cardiac muscle / intercellular bridge ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / glutathione binding / hepoxilin biosynthetic process / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / relaxation of cardiac muscle / intercellular bridge / positive regulation of ryanodine-sensitive calcium-release channel activity / cellular response to caffeine / glutathione transferase / glutathione transferase activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / glutathione metabolic process / sarcoplasmic reticulum / fatty acid binding / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutathione S-transferase Mu 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPatskovska, L.N. / Fedorov, A.A. / Patskovsky, Y.V. / Almo, S.C. / Listowsky, I.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: The enhanced affinity for thiolate anion and activation of enzyme-bound glutathione is governed by an arginine residue of human Mu class glutathione S-transferases.
Authors: Patskovsky, Y.V. / Patskovska, L.N. / Listowsky, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Expression, Crystallization and Preliminary X-Ray Analysis of Ligand-Free Human Glutathione S-Transferase M2-2
Authors: Patskovska, L.N. / Fedorov, A.A. / Patskovsky, Y.V. / Almo, S.C. / Listowsky, I.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal Structure of Human Class Mu Glutathione Transferase Gstm2-2. Effects of Lattice Packing on Conformational Heterogeneity
Authors: Raghunathan, S. / Chandross, R.J. / Kretsinger, R.H. / Allison, T.J. / Penington, C.J. / Rule, G.S.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Cloning, Expression, and Characterization of a Class-Mu Glutathione Transferase from Human Muscle, the Product of the Gst4 Locus
Authors: Vorachek, W.R. / Pearson, W.R. / Rule, G.S.
History
DepositionMay 26, 1998Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)51,2912
Polymers51,2912
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-9 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.909, 81.479, 55.621
Angle α, β, γ (deg.)90.00, 109.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.187925, 0.958163, 0.215887), (0.959859, 0.132565, 0.247177), (0.208217, 0.253672, -0.944614)
Vector: -25.00254, 4.13498, 77.34892)

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE


Mass: 25645.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: LIGAND-FREE / Source: (gene. exp.) Homo sapiens (human)
Description: THE GSTM2 CDNA WAS AMPLIFIED USING RT-PCR AND SUBCLONED INTO A PET3A EXPRESSION VECTOR
Cell line: HELA / Cellular location: CYTOPLASM / Gene: GSTM2 / Plasmid: PET3A-GSTM2 / Species (production host): Escherichia coli / Gene (production host): GSTM2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P28161, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Patskovska, L.N., (1998) Acta Crystallogr.,Sect.D, 54, 458.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115-31 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
30.2 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→10 Å / Num. obs: 12321 / % possible obs: 84.15 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.5
Reflection shellResolution: 2.55→3 Å / Redundancy: 1.55 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 4.2 / % possible all: 48
Reflection
*PLUS
Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Rmerge(I) obs: 0.097

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HNA

1hna


Resolution: 2.55→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.257 575 4.87 %RANDOM
Rwork0.203 ---
obs0.203 11894 81.2 %-
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-10 Å
Refinement stepCycle: LAST / Resolution: 2.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 0 57 3671
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.381
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.411
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.531.5
X-RAY DIFFRACTIONx_mcangle_it2.472
X-RAY DIFFRACTIONx_scbond_it2.62
X-RAY DIFFRACTIONx_scangle_it4.022.5
LS refinement shellResolution: 2.55→2.66 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.315 32 6.1 %
Rwork0.243 525 -
obs--30.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.SOLV
X-RAY DIFFRACTION2PARAM19.SOLVTOPHCSDX.PRO
Refinement
*PLUS
Rfactor obs: 0.203 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.507
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.411
LS refinement shell
*PLUS
Rfactor Rfree: 0.315 / Rfactor Rwork: 0.243 / Rfactor obs: 0.243

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