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- PDB-2vct: Glutathione transferase A2-2 in complex with delta-4-andostrene-3... -

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Basic information

Entry
Database: PDB / ID: 2vct
TitleGlutathione transferase A2-2 in complex with delta-4-andostrene-3-17- dione
ComponentsGLUTATHIONE S-TRANSFERASE A2
KeywordsTRANSFERASE / ANDOSTRENE DIONE / STEROID METABOLISM / 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
4-ANDROSTENE-3-17-DIONE / Glutathione S-transferase A2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionSep 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2008Provider: 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 1.4Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 1.5Dec 13, 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 A2
B: GLUTATHIONE S-TRANSFERASE A2
C: GLUTATHIONE S-TRANSFERASE A2
D: GLUTATHIONE S-TRANSFERASE A2
E: GLUTATHIONE S-TRANSFERASE A2
F: GLUTATHIONE S-TRANSFERASE A2
G: GLUTATHIONE S-TRANSFERASE A2
H: GLUTATHIONE S-TRANSFERASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,86612
Polymers205,7208
Non-polymers1,1464
Water29,2741625
1
A: GLUTATHIONE S-TRANSFERASE A2
B: GLUTATHIONE S-TRANSFERASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0034
Polymers51,4302
Non-polymers5732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-24 kcal/mol
Surface area20920 Å2
MethodPISA
2
C: GLUTATHIONE S-TRANSFERASE A2
D: GLUTATHIONE S-TRANSFERASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0034
Polymers51,4302
Non-polymers5732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-24.6 kcal/mol
Surface area21110 Å2
MethodPISA
3
E: GLUTATHIONE S-TRANSFERASE A2
F: GLUTATHIONE S-TRANSFERASE A2


Theoretical massNumber of molelcules
Total (without water)51,4302
Polymers51,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-23 kcal/mol
Surface area21050 Å2
MethodPISA
4
G: GLUTATHIONE S-TRANSFERASE A2
H: GLUTATHIONE S-TRANSFERASE A2


Theoretical massNumber of molelcules
Total (without water)51,4302
Polymers51,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-23.5 kcal/mol
Surface area20910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.546, 97.343, 110.302
Angle α, β, γ (deg.)90.00, 115.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.14943, 0.76184, -0.63029), (0.74483, -0.50598, -0.43499), (-0.65031, -0.40445, -0.64305)39.841, -70.56317, -11.58124
2given(0.48901, -0.00317, -0.87227), (0.00073, -0.99999, 0.00404), (-0.87228, -0.00261, -0.48901)29.55214, -46.24124, 50.09357
3given(0.62526, -0.7608, 0.17387), (0.73873, 0.50515, -0.44621), (0.25165, 0.40744, 0.87787)58.77888, 24.29273, 20.52604
4given(-0.00988, 0.85131, -0.52458), (0.83664, -0.28028, -0.47062), (-0.54767, -0.44353, -0.70946)89.4124, -35.63917, -25.73468
5given(0.98541, 0.16923, -0.01835), (-0.16701, 0.98202, 0.08798), (0.03291, -0.08363, 0.99595)37.17848, 23.80718, -7.79124
6given(0.48875, -0.21038, -0.84668), (-0.20382, -0.97117, 0.12365), (-0.84828, 0.11214, -0.51754)21.91974, -21.23728, -32.58512
7given(0.42505, -0.86132, 0.27831), (0.82839, 0.24623, -0.50313), (0.36482, 0.44441, 0.81817)65.44708, 36.18267, -70.39578

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Components

#1: Protein
GLUTATHIONE S-TRANSFERASE A2 / 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-ASD / 4-ANDROSTENE-3-17-DIONE / Androstenedione


Mass: 286.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H26O2 / Comment: hormone*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1625 / 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: 2.28 Å3/Da / Density % sol: 45.56 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.8
Details: HANGING DROP VAPOUR TECHNIQUE WAS USED. 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WAS MIXED WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN ...Details: HANGING DROP VAPOUR TECHNIQUE WAS USED. 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WAS MIXED WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1UL OF 20 MM ANDROSTENE DIONE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 25, 2006 / Details: MIRRORS
RadiationMonochromator: DOUBLE SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 111829 / % possible obs: 99.8 % / Observed criterion σ(I): 1.6 / Redundancy: 3.6 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

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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 2VCR

2vcr
PDB Unreleased entry


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.87 / SU B: 6.939 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 5956 5.1 %RANDOM
Rwork0.217 ---
obs0.221 111829 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-2.28 Å2
2---1.44 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14400 0 84 1625 16109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02214776
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4322.01119892
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6851760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34224.39656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.434152920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0951588
X-RAY DIFFRACTIONr_chiral_restr0.0940.22188
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210840
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.27616
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.210100
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.21416
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.2109
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6641.59268
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.095214288
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63536348
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.424.55604
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 450
Rwork0.246 8167

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