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- PDB-3gtu: LIGAND-FREE HETERODIMERIC HUMAN GLUTATHIONE S-TRANSFERASE M2-3 (E... -

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Basic information

Entry
Database: PDB / ID: 3gtu
TitleLIGAND-FREE HETERODIMERIC HUMAN GLUTATHIONE S-TRANSFERASE M2-3 (EC 2.5.1.18), MONOCLINIC CRYSTAL FORM
Components(GLUTATHIONE S-TRANSFERASE) x 2
KeywordsTRANSFERASE / GLUTATHIONE / CONJUGATION / DETOXIFICATION / CYTOSOLIC / HETERODIMER
Function / homology
Function and homology information


establishment of blood-nerve barrier / sperm fibrous sheath / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione binding / glutathione derivative biosynthetic process / linoleic acid metabolic process / Glutathione conjugation ...establishment of blood-nerve barrier / sperm fibrous sheath / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione binding / glutathione derivative 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 / glutathione metabolic process / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / sarcoplasmic reticulum / fatty acid binding / response to estrogen / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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 3 / Glutathione S-transferase Mu 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPatskovsky, Y.V. / Patskovska, L.N. / Listowsky, I.
Citation
Journal: Biochemistry / Year: 1999
Title: An asparagine-phenylalanine substitution accounts for catalytic differences between hGSTM3-3 and other human class mu glutathione S-transferases.
Authors: Patskovsky, Y.V. / Patskovska, L.N. / Listowsky, I.
#1: 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.
#2: 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.
#3: Journal: J.Biol.Chem. / Year: 1990
Title: A Distinct Human Testis and Brain Mu-Class Glutathione S-Transferase. Molecular Cloning and Characterization of a Form Present Even in Individuals Lacking Hepatic Type Mu Isoenzymes
Authors: Campbell, E. / Takahashi, Y. / Abramovitz, M. / Peretz, M. / Listowsky, I.
History
DepositionJul 29, 1998Processing site: BNL
Revision 1.0Jul 29, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: 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: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
C: GLUTATHIONE S-TRANSFERASE
D: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)104,2124
Polymers104,2124
Non-polymers00
Water1,29772
1
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)52,1062
Polymers52,1062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-11 kcal/mol
Surface area19690 Å2
MethodPISA
2
C: GLUTATHIONE S-TRANSFERASE
D: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)52,1062
Polymers52,1062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-11 kcal/mol
Surface area19770 Å2
MethodPISA
3
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE

C: GLUTATHIONE S-TRANSFERASE
D: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)104,2124
Polymers104,2124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area6360 Å2
ΔGint-35 kcal/mol
Surface area38330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.970, 102.747, 103.977
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999976, 0.004042, -0.005642), (0.001042, 0.891131, 0.453745), (0.006862, 0.453728, -0.891114)-23.8989, -62.3432, 155.6123
2given(-0.999999, 0.001036, -3.5E-5), (0.000905, 0.889089, 0.457734), (0.000505, 0.457734, -0.889089)-24.4275, -62.873, 155.42059

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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, HETERODIMER / Source: (gene. exp.) Homo sapiens (human)
Description: THE GSTM2 AND GSTM3 CDNA WERE AMPLIFIED USING RT-PCR AND SUBCLONED INTO A PET3A COEXPRESSION VECTOR. SYNTHETIC GENE.
Cell line: HELA / Cellular location: CYTOPLASM / Gene: GSTM2, GSTM3 / Plasmid: PET3A-GSTM2-3 / Species (production host): Escherichia coli / Gene (production host): GSTM2, GSTM3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P28161, glutathione transferase
#2: Protein GLUTATHIONE S-TRANSFERASE /


Mass: 26460.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: LIGAND-FREE, HETERODIMER / Source: (gene. exp.) Homo sapiens (human)
Description: THE GSTM2 AND GSTM3 CDNA WERE AMPLIFIED USING RT-PCR AND SUBCLONED INTO A PET3A COEXPRESSION VECTOR. SYNTHETIC GENE.
Cell line: HELA / Cellular location: CYTOPLASM / Gene: GSTM2, GSTM3 / Plasmid: PET3A-GSTM2-3 / Species (production host): Escherichia coli / Gene (production host): GSTM2, GSTM3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P21266, glutathione transferase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.65 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jul 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→10 Å / Num. obs: 25387 / % possible obs: 94.41 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 3.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.71 % / Rmerge(I) obs: 0.341 / % possible all: 69.4

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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 2GTU

2gtu


Resolution: 2.8→8 Å / Rfactor Rfree error: 0.01 / 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
Rfree0.27 996 4.96 %RANDOM
Rwork0.225 ---
obs0.225 20086 78.14 %-
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-8 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7328 0 0 72 7400
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.18
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.11
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.053
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.771.5
X-RAY DIFFRACTIONx_mcangle_it2.862
X-RAY DIFFRACTIONx_scbond_it2.672
X-RAY DIFFRACTIONx_scangle_it3.952.5
LS refinement shellResolution: 2.8→2.92 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.27 64 5.04 %
Rwork0.26 1205 -
obs--39.52 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.SOLV
X-RAY DIFFRACTION2PARAM19.SOLVTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.11
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.053

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