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- PDB-1gtu: LIGAND-FREE HUMAN GLUTATHIONE S-TRANSFERASE M1A-1A -

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Basic information

Entry
Database: PDB / ID: 1gtu
TitleLIGAND-FREE HUMAN GLUTATHIONE S-TRANSFERASE M1A-1A
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / GLUTATHIONE / CONJUGATION / DETOXIFICATION / CYTOSOLIC / DIMER
Function / homology
Function and homology information


nitrobenzene metabolic process / cellular detoxification of nitrogen compound / glutathione derivative biosynthetic process / glutathione binding / hepoxilin biosynthetic process / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / intercellular bridge ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / glutathione derivative biosynthetic process / glutathione binding / hepoxilin biosynthetic process / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / intercellular bridge / glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / glutathione metabolic process / enzyme binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / 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 ...Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsPatskovsky, Y.V. / Patskovska, L.N. / Listowsky, I.
Citation
Journal: Biochemistry / Year: 1999
Title: Functions of His107 in the catalytic mechanism of human glutathione S-transferase hGSTM1a-1a.
Authors: Patskovsky, Y.V. / Patskovska, L.N. / Listowsky, I.
#1: Journal: Biochem.J. / Year: 1993
Title: Deduced Amino Acid Sequence, Gene Structure and Chromosomal Location of a Novel Human Class Mu Glutathione S-Transferase, Gstm4
Authors: Zhong, S. / Spurr, N.K. / Hayes, J.D. / Wolf, C.R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Hereditary Differences in the Expression of the Human Glutathione Transferase Active on Trans-Stilbene Oxide are due to a Gene Deletion
Authors: Seidegard, J. / Vorachek, W.R. / Pero, R.W. / Pearson, W.R.
#3: Journal: Nucleic Acids Res. / Year: 1988
Title: The Human Liver Glutathione S-Transferase Gene Superfamily: Expression and Chromosome Mapping of an Hb Subunit Cdna
Authors: Dejong, J.L. / Chang, C.M. / Whang-Peng, J. / Knutsen, T. / TU, C.P.
History
DepositionJun 11, 1998Processing site: BNL
Revision 1.0Feb 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 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)102,4634
Polymers102,4634
Non-polymers00
Water1,13563
1
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)51,2312
Polymers51,2312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-19 kcal/mol
Surface area19530 Å2
MethodPISA
2
C: GLUTATHIONE S-TRANSFERASE
D: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)51,2312
Polymers51,2312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-19 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.957, 84.987, 215.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.060197, 0.990072, -0.127018), (0.990961, -0.074559, -0.111523), (-0.119886, -0.119157, -0.985611)-11.3206, 46.8672, 276.99261
2given(-0.991927, -0.017607, -0.125581), (-0.000539, 0.990891, -0.134665), (0.126808, -0.13351, -0.982901)52.9508, 25.8623, 326.6691
3given(-0.078008, 0.996742, -0.020501), (-0.996915, -0.078167, -0.007078), (-0.008657, 0.019886, 0.999765)-23.2152, 61.4653, -54.5606

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Components

#1: Protein
GLUTATHIONE S-TRANSFERASE


Mass: 25615.646 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: LIGAND-FREE / Source: (gene. exp.) Homo sapiens (human)
Description: THE GSTM1A CDNA WAS AMPLIFIED USING RT-PCR AND SUBCLONED INTO A PET3A EXPRESSION VECTOR
Cell line: HELA / Cellular location: CYTOPLASM / Gene: GSTM1A / Organ: LIVER / Plasmid: PET3A-GSTM1A / Species (production host): Escherichia coli / Gene (production host): GSTM1A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P09488, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 58 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 289 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116-20 mg/mlprotein1drop
210 mMTris-HCl1drop
30.2 mMdithiothreitol1drop
416-22 %PEG40001reservoir
550 mM1reservoirKH2PO4
625 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Apr 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.68→12.35 Å / Num. obs: 26217 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.058
Reflection shellResolution: 2.68→2.9 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.155 / % possible all: 87.1
Reflection shell
*PLUS
% possible obs: 87.1 %

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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: 2.68→10 Å / Rfactor Rfree error: 0.008 / 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
Rfree0.245 2268 9.9 %RANDOM
Rwork0.211 ---
obs0.211 23012 77.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-10 Å
Refinement stepCycle: LAST / Resolution: 2.68→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7216 0 0 64 7280
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.32
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.02
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.41
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.541.5
X-RAY DIFFRACTIONx_mcangle_it2.562
X-RAY DIFFRACTIONx_scbond_it2.572
X-RAY DIFFRACTIONx_scangle_it42.5
LS refinement shellResolution: 2.68→2.8 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.28 139 9.55 %
Rwork0.245 1316 -
obs--40.1 %
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.02
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.41

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