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- PDB-2c4j: Human glutathione-S-transferase M2-2 T210S mutant in complex with... -

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Basic information

Entry
Database: PDB / ID: 2c4j
TitleHuman glutathione-S-transferase M2-2 T210S mutant in complex with glutathione-styrene oxide conjugate
ComponentsGLUTATHIONE S-TRANSFERASE MU 2
KeywordsTRANSFERASE / GLUTATHIONE / GLUTATHIONE TRANSFERASE / M2-2 / MULTIGENE FAMILY
Function / homology
Function and homology information


nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione binding / linoleic acid metabolic process / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / Glutathione conjugation / glutathione peroxidase activity / relaxation of cardiac muscle / cellular response to caffeine ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione binding / linoleic acid metabolic process / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / Glutathione conjugation / glutathione peroxidase activity / relaxation of cardiac muscle / cellular response to caffeine / glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / intercellular bridge / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / glutathione metabolic process / sarcoplasmic reticulum / fatty acid binding / transmembrane transporter 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 / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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
Chem-GSO / Glutathione S-transferase Mu 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsTars, K. / Andersson, M. / Ivarsson, Y. / Olin, B. / Mannervik, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Alternative Mutations of a Positively Selected Residue Elicit Gain or Loss of Functionalities in Enzyme Evolution.
Authors: Norrgard, M.A. / Ivarsson, Y. / Tars, K. / Mannervik, B.
History
DepositionOct 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)104,7608
Polymers103,0514
Non-polymers1,7104
Water17,330962
1
A: GLUTATHIONE S-TRANSFERASE MU 2
B: GLUTATHIONE S-TRANSFERASE MU 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3804
Polymers51,5252
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: GLUTATHIONE S-TRANSFERASE MU 2
D: GLUTATHIONE S-TRANSFERASE MU 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3804
Polymers51,5252
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.176, 67.768, 115.705
Angle α, β, γ (deg.)90.00, 99.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.852781, 0.438924, -0.283036), (0.440416, 0.31309, -0.841432), (-0.280709, -0.842212, -0.460307)23.65083, 84.65993, 144.58746
2given(-0.025996, -0.680145, -0.732616), (0.067082, -0.732399, 0.677563), (-0.997409, -0.031531, 0.064665)40.44772, 9.09136, 100.51621
3given(-0.106819, 0.337401, 0.935281), (-0.605151, -0.768432, 0.208096), (0.788912, -0.543758, 0.286262)-33.81146, 22.68296, 78.29236

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Components

#1: Protein
GLUTATHIONE S-TRANSFERASE MU 2 / GLUTATHIONE TRANSFERASE M2-1 / GSTM2-2 / GST CLASS-MU 2


Mass: 25762.627 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P28161, glutathione transferase
#2: Chemical
ChemComp-GSO / L-GAMMA-GLUTAMYL-S-[(2S)-2-HYDROXY-2-PHENYLETHYL]-L-CYSTEINYLGLYCINE


Mass: 427.472 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H25N3O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 962 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONJUGATES REDUCED GLUTATHIONE TO A LARGE NUMBER OF EXOGENOUS AND ENDOGENOUS HYDROPHOBIC ...CONJUGATES REDUCED GLUTATHIONE TO A LARGE NUMBER OF EXOGENOUS AND ENDOGENOUS HYDROPHOBIC ELECTROPHILES. ENGINEERED RESIDUE IN CHAIN A, THR 209 TO SER ENGINEERED RESIDUE IN CHAIN B, THR 209 TO SER ENGINEERED RESIDUE IN CHAIN C, THR 209 TO SER ENGINEERED RESIDUE IN CHAIN D, THR 209 TO SER
Sequence detailsRESIDUE THR 210 IS MUTATED TO SERINE

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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: 2.06 Å3/Da / Density % sol: 39.92 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP VAPOUR TECHNIQUE. 5 MICRLITRES OF PROTEIN AT 10MG/ML IN 20 MM TRIS-HCL, PH 8.0 WERE MIXED WITH 5 MICROLITRES OF RESERVOIR SOLUTION CONTAINING 100 MM TRIS-HCL, PH 7.8, 2MM DTT, ...Details: HANGING DROP VAPOUR TECHNIQUE. 5 MICRLITRES OF PROTEIN AT 10MG/ML IN 20 MM TRIS-HCL, PH 8.0 WERE MIXED WITH 5 MICROLITRES OF RESERVOIR SOLUTION CONTAINING 100 MM TRIS-HCL, PH 7.8, 2MM DTT, 25% PEG 4000 AND 1 MICROLITRE OF 20MM GLUTATHIONE CONJUGATE WITH STYRENE OXIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 194076 / % possible obs: 98.2 % / Observed criterion σ(I): 2.8 / Redundancy: 3.2 % / Biso Wilson estimate: 14.05 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.8 / % possible all: 87.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GTU

2gtu


Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.032 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 10227 5 %RANDOM
Rwork0.194 ---
obs0.195 194076 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å2-0.1 Å2
2---0.31 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7224 0 116 962 8302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227563
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.98810189
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.755864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99624.118374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13151375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3121544
X-RAY DIFFRACTIONr_chiral_restr0.0810.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025768
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.23648
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.25197
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2812
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8471.54500
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23827037
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.88733528
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9824.53152
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 661 -
Rwork0.292 13042 -
obs--89.84 %

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