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- PDB-1ykc: human glutathione S-transferase m2-2 (E.C.2.5.1.18) complexed wit... -

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Basic information

Entry
Database: PDB / ID: 1ykc
Titlehuman glutathione S-transferase m2-2 (E.C.2.5.1.18) complexed with glutathione-disulfide
ComponentsGlutathione S-transferase Mu 2
KeywordsTRANSFERASE / glutathione / conjugation / glutathione-disulfide / prostaglandin E2 / synthase
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
OXIDIZED GLUTATHIONE DISULFIDE / Glutathione S-transferase Mu 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPatskovsky, Y.V. / Patskovska, L.N. / Listowsky, I. / Almo, S.C.
Citation
Journal: To be Published
Title: Selective Inhibitors of Prostaglandin Synthase activity of human glutathione S-transferase M2-2
Authors: Patskovsky, Y.V. / Patskovska, L.N. / Listowsky, I. / Almo, S.C.
#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
DepositionJan 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: 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)52,5164
Polymers51,2912
Non-polymers1,2252
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-12 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.610, 74.790, 116.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homodimer. The asymmetric unit contains one full homodimer (chains A and B)

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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-GDS / OXIDIZED GLUTATHIONE DISULFIDE


Mass: 612.631 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32N6O12S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.37 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG4000, pH 6.50, VAPOR DIFFUSION, SITTING DROP, 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: Nov 21, 2004 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 28914 / Num. obs: 28914 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.076 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3320 / Rsym value: 0.25 / % possible all: 86.9

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Processing

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

2gtu


Resolution: 2.1→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 152191.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 846 3.1 %RANDOM
Rwork0.206 ---
all0.225 28914 --
obs0.206 27617 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.0906 Å2 / ksol: 0.253515 e/Å3
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.95 Å20 Å20 Å2
2--5.22 Å20 Å2
3----0.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 80 396 4090
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d1.34
X-RAY DIFFRACTIONc_mcbond_it2.182
X-RAY DIFFRACTIONc_mcangle_it3.863.5
X-RAY DIFFRACTIONc_scbond_it3.053.5
X-RAY DIFFRACTIONc_scangle_it5.314.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 143 3.8 %
Rwork0.263 3663 -
obs-3663 78.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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