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- PDB-1xw5: Human glutathione s-transferase M2-2 (E.C.2.5.1.18)complexed with... -

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Basic information

Entry
Database: PDB / ID: 1xw5
TitleHuman glutathione s-transferase M2-2 (E.C.2.5.1.18)complexed with glutathione, monoclinic crystal form
ComponentsGlutathione S-transferase Mu 2
KeywordsTRANSFERASE / GLUTATHIONE / CONJUGATION / DETOXIFICATION / CYTOSOLIC / DIMER / ACTIVE SITE
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 / hepoxilin biosynthetic process / glutathione binding / 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 / hepoxilin biosynthetic process / glutathione binding / 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 / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular exosome / 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 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 / Glutathione S-transferase Mu 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPatskovska, L.N. / Patskovsky, Y.V. / Almo, S.C. / Listowsky, I.
Citation
Journal: To be Published
Title: Structural Perturbation of the Active Site of Human Glutathione-S-Transferase M2-2 Upon Ligand Binding
Authors: Patskovsky, Y. / Patskovska, L.N. / Almo, S.C. / 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
DepositionOct 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase Mu 2
B: Glutathione S-transferase Mu 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9064
Polymers51,2912
Non-polymers6152
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-16 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.200, 49.790, 92.040
Angle α, β, γ (deg.)90.00, 94.27, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological unit is a homodimer, the assymetric unit contains homodimer

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Components

#1: Protein Glutathione S-transferase Mu 2 / GSTM2-2 / GST class-mu 2


Mass: 25645.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTM2, GST4 / Plasmid: peT3a-hGSTM2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P28161, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.25 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG4000, pH 6.50, VAPOR DIFFUSION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 11, 2004 / Details: MIRRORS
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 43318 / Num. obs: 38664 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.062 / Net I/σ(I): 11.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.017 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1864 / Rsym value: 0.019 / % possible all: 43.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CCP4model building
CNS1refinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GTU

2gtu


Resolution: 1.8→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1160 3 %RANDOM
Rwork0.206 ---
all0.22 38611 --
obs0.206 38283 88.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.4053 Å2 / ksol: 0.318977 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.41 Å20 Å21.29 Å2
2--4.85 Å20 Å2
3----0.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-6 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 40 461 4115
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_mcbond_it1.862
X-RAY DIFFRACTIONc_mcangle_it3.293
X-RAY DIFFRACTIONc_scbond_it2.593
X-RAY DIFFRACTIONc_scangle_it4.644
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 99 2.8 %
Rwork0.28 3491 -
obs-3491 50.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3GSHPARAM.PEPGSHTOP.PEP

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