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- PDB-2ab6: HUMAN GLUTATHIONE S-TRANSFERASE M2-2 (E.C.2.5.1.18) complexed wit... -

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Basic information

Entry
Database: PDB / ID: 2ab6
TitleHUMAN GLUTATHIONE S-TRANSFERASE M2-2 (E.C.2.5.1.18) complexed with S-METHYLGLUTATHIONE
ComponentsGlutathione S-transferase Mu 2
KeywordsTRANSFERASE / S-METHYLGLUTATHIONE / CONJUGATION / DETOXIFICATION
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
L-GAMMA-GLUTAMYL-S-METHYLCYSTEINYLGLYCINE / Glutathione S-transferase Mu 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPatskovsky, Y. / Almo, S.C. / Listowsky, I.
Citation
Journal: To be Published
Title: Structural Perturbations in the Active Site of Human Glutathione-S-Transferase M2-2 Upon Ligand Binding
Authors: Patskovsky, Y. / Patskovska, L. / 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
DepositionJul 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
C: Glutathione S-transferase Mu 2
D: Glutathione S-transferase Mu 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8678
Polymers102,5824
Non-polymers1,2854
Water3,657203
1
A: Glutathione S-transferase Mu 2
B: Glutathione S-transferase Mu 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9344
Polymers51,2912
Non-polymers6432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-15 kcal/mol
Surface area18620 Å2
MethodPISA
2
C: Glutathione S-transferase Mu 2
D: Glutathione S-transferase Mu 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9344
Polymers51,2912
Non-polymers6432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-16 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.120, 76.716, 212.449
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 1 - 217 / Label seq-ID: 1 - 217

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe biological assembly is a homodimer composed of two identical monomers. The asymmetric unit contains two homodimers, composed of chains A/B and C/D, respectively.

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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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTM2, GST4 / Plasmid: pET3a-GSTM2 / 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-GSM / L-GAMMA-GLUTAMYL-S-METHYLCYSTEINYLGLYCINE / S-METHYL-GLUTATHIONE


Mass: 321.350 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H19N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.17 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 4000, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 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: 2.5→20 Å / Num. all: 28327 / Num. obs: 28327 / % possible obs: 86.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.13 / Net I/σ(I): 3
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3927 / Rsym value: 0.41 / % possible all: 73.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CCP4model building
REFMAC5.2.0005refinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GTU

2gtu


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.814 / SU B: 14.608 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27961 903 3.2 %RANDOM
Rwork0.22866 ---
all0.252 28296 --
obs0.23029 27393 86.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.864 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2--0.61 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7228 0 84 203 7515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227500
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.98310108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0085864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33424.086372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.061151356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1041544
X-RAY DIFFRACTIONr_chiral_restr0.1030.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025732
X-RAY DIFFRACTIONr_nbd_refined0.1860.33540
X-RAY DIFFRACTIONr_nbtor_refined0.3150.55126
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.5514
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.330.396
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3670.511
X-RAY DIFFRACTIONr_mcbond_it1.49324438
X-RAY DIFFRACTIONr_mcangle_it2.40537016
X-RAY DIFFRACTIONr_scbond_it1.66123470
X-RAY DIFFRACTIONr_scangle_it2.74233092
Refine LS restraints NCS

Ens-ID: 1 / Number: 1828 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.050.05
3Ctight positional0.060.05
4Dtight positional0.050.05
1Atight thermal0.10.5
2Btight thermal0.090.5
3Ctight thermal0.090.5
4Dtight thermal0.10.5
LS refinement shellResolution: 2.5→2.56 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 54 -
Rwork0.349 1541 -
obs-1541 67.24 %

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