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- PDB-2wju: Glutathione transferase A2-2 in complex with glutathione -

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Basic information

Entry
Database: PDB / ID: 2wju
TitleGlutathione transferase A2-2 in complex with glutathione
ComponentsGLUTATHIONE-S-TRANSFERASE A2-2
KeywordsTRANSFERASE / GLUTATHIONE
Function / homology
Function and homology information


Glutathione conjugation / Azathioprine ADME / glutathione transferase / glutathione transferase activity / glutathione metabolic process / epithelial cell differentiation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / xenobiotic metabolic process / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha 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, alpha 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 A2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTars, K. / Olin, B. / Mannervik, B.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Basis for Featuring of Steroid Isomerase Activity in Alpha Class Glutathione Transferases.
Authors: Tars, K. / Olin, B. / Mannervik, B.
History
DepositionMay 29, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionJun 9, 2009ID: 2VCR
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 A2-2
B: GLUTATHIONE-S-TRANSFERASE A2-2
C: GLUTATHIONE-S-TRANSFERASE A2-2
D: GLUTATHIONE-S-TRANSFERASE A2-2
E: GLUTATHIONE-S-TRANSFERASE A2-2
F: GLUTATHIONE-S-TRANSFERASE A2-2
G: GLUTATHIONE-S-TRANSFERASE A2-2
H: GLUTATHIONE-S-TRANSFERASE A2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,17916
Polymers205,7208
Non-polymers2,4598
Water10,034557
1
A: GLUTATHIONE-S-TRANSFERASE A2-2
B: GLUTATHIONE-S-TRANSFERASE A2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0454
Polymers51,4302
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-24.9 kcal/mol
Surface area20340 Å2
MethodPISA
2
C: GLUTATHIONE-S-TRANSFERASE A2-2
D: GLUTATHIONE-S-TRANSFERASE A2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0454
Polymers51,4302
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-24.2 kcal/mol
Surface area20430 Å2
MethodPISA
3
E: GLUTATHIONE-S-TRANSFERASE A2-2
F: GLUTATHIONE-S-TRANSFERASE A2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0454
Polymers51,4302
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-28.3 kcal/mol
Surface area20230 Å2
MethodPISA
4
G: GLUTATHIONE-S-TRANSFERASE A2-2
H: GLUTATHIONE-S-TRANSFERASE A2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0454
Polymers51,4302
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-27.1 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.160, 85.500, 113.420
Angle α, β, γ (deg.)96.00, 101.78, 97.46
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.708637, -0.6761, -0.201796), (-0.681857, 0.582683, 0.442212), (-0.181396, 0.450964, -0.873915)0.00493, 0.12267, -0.33464
2given(-0.714432, 0.699411, 0.020277), (0.699679, 0.713858, 0.029269), (0.005996, 0.035099, -0.999366)23.99184, -39.37238, -16.29606
3given(0.016149, -0.987987, 0.153692), (0.895606, -0.054049, -0.441552), (0.444555, 0.144779, 0.883974)24.15715, -39.1705, -15.89721
4given(0.281425, 0.894056, 0.348516), (-0.959391, 0.254885, 0.12084), (0.019206, -0.368371, 0.92948)-9.2749, -45.24642, 37.8125
5given(0.449055, -0.732726, -0.511334), (-0.735214, -0.628222, 0.254555), (-0.50775, 0.26163, -0.820816)-9.37805, -45.02482, 37.42079
6given(-0.839739, 0.076147, 0.537625), (-0.219641, -0.953135, -0.208067), (0.496585, -0.292807, 0.817109)-29.47962, -87.08466, 56.36354
7given(0.655126, 0.64784, -0.388733), (0.663567, -0.739391, -0.113928), (-0.361233, -0.183313, -0.91428)-30.01229, -87.18108, 56.08477

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Components

#1: Protein
GLUTATHIONE-S-TRANSFERASE A2-2 / GLUTATHIONE-S-TRANSFERASE A2-2 / GTH2 / HA SUBUNIT 2 / GST-GAMMA / GSTA2-2 / GST CLASS-ALPHA MEMBER 2


Mass: 25715.006 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL BLUE / References: UniProt: P09210, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsS112T IS A NATURAL VARIANT

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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: 2.39 Å3/Da / Density % sol: 48.06 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: THE CRYSTALS WERE OBTAINED BY HANGING DROP VAPOUR TECHNIQUE BY MIXING 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WITH 5 UL OF PROTEIN ...Details: THE CRYSTALS WERE OBTAINED BY HANGING DROP VAPOUR TECHNIQUE BY MIXING 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1 UL OF 25 MM GLUTATHIONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→42 Å / Num. obs: 79974 / % possible obs: 92 % / Observed criterion σ(I): 2.5 / Redundancy: 1.9 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.5 / % possible all: 65

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VCV

2vcv


Resolution: 2.3→42 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.857 / SU B: 10.37 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.588 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29735 4027 5 %RANDOM
Rwork0.24558 ---
obs0.24811 75947 91.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.954 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.07 Å2-0.27 Å2
2--0.04 Å2-0.01 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14400 0 160 557 15117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02214832
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1722.01219928
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.40551760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25824.39656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.116152920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4141588
X-RAY DIFFRACTIONr_chiral_restr0.0730.22184
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210920
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.27187
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.210069
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2759
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4361.59226
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.778214288
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.85336378
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3254.55640
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 205 -
Rwork0.293 3669 -
obs--59.77 %

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