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- PDB-2vcv: Glutathione transferase A3-3 in complex with glutathione and delt... -

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Basic information

Entry
Database: PDB / ID: 2vcv
TitleGlutathione transferase A3-3 in complex with glutathione and delta-4- androstene-3-17-dione
ComponentsGLUTATHIONE S-TRANSFERASE A3
KeywordsTRANSFERASE / ANDOSTRENE DIONE / STEROID METABOLISM / GLUTATHIONE
Function / homology
Function and homology information


Glutathione conjugation / NFE2L2 regulating anti-oxidant/detoxification enzymes / glutathione transferase / glutathione transferase activity / glutathione metabolic process / xenobiotic metabolic process / lipid metabolic process / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / : / 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 ...Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / : / 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
4-ANDROSTENE-3-17-DIONE / GLUTATHIONE / Glutathione S-transferase A3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1Feb 29, 2012Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.2May 29, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
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 A3
B: GLUTATHIONE S-TRANSFERASE A3
C: GLUTATHIONE S-TRANSFERASE A3
D: GLUTATHIONE S-TRANSFERASE A3
E: GLUTATHIONE S-TRANSFERASE A3
F: GLUTATHIONE S-TRANSFERASE A3
G: GLUTATHIONE S-TRANSFERASE A3
H: GLUTATHIONE S-TRANSFERASE A3
I: GLUTATHIONE S-TRANSFERASE A3
J: GLUTATHIONE S-TRANSFERASE A3
K: GLUTATHIONE S-TRANSFERASE A3
L: GLUTATHIONE S-TRANSFERASE A3
M: GLUTATHIONE S-TRANSFERASE A3
N: GLUTATHIONE S-TRANSFERASE A3
O: GLUTATHIONE S-TRANSFERASE A3
P: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,48743
Polymers405,41916
Non-polymers8,06827
Water58,7833263
1
A: GLUTATHIONE S-TRANSFERASE A3
B: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8656
Polymers50,6772
Non-polymers1,1874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-24.1 kcal/mol
Surface area19420 Å2
MethodPISA
2
C: GLUTATHIONE S-TRANSFERASE A3
D: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5785
Polymers50,6772
Non-polymers9013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-25.8 kcal/mol
Surface area19910 Å2
MethodPISA
3
E: GLUTATHIONE S-TRANSFERASE A3
F: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8656
Polymers50,6772
Non-polymers1,1874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-23.1 kcal/mol
Surface area19440 Å2
MethodPISA
4
G: GLUTATHIONE S-TRANSFERASE A3
H: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8656
Polymers50,6772
Non-polymers1,1874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-23.3 kcal/mol
Surface area19420 Å2
MethodPISA
5
I: GLUTATHIONE S-TRANSFERASE A3
J: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5785
Polymers50,6772
Non-polymers9013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-25.7 kcal/mol
Surface area19840 Å2
MethodPISA
6
K: GLUTATHIONE S-TRANSFERASE A3
L: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8656
Polymers50,6772
Non-polymers1,1874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-21.5 kcal/mol
Surface area19490 Å2
MethodPISA
7
M: GLUTATHIONE S-TRANSFERASE A3
N: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2924
Polymers50,6772
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-28 kcal/mol
Surface area19970 Å2
MethodPISA
8
O: GLUTATHIONE S-TRANSFERASE A3
P: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5785
Polymers50,6772
Non-polymers9013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-24 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.177, 92.064, 113.540
Angle α, β, γ (deg.)89.76, 89.72, 89.73
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.92867, -0.37048, 0.01777), (-0.37086, 0.92824, -0.02884), (-0.00581, -0.03338, -0.99943)-78.02039, -14.43444, 31.83014
2given(0.94187, 0.3358, -0.01094), (0.33481, -0.9408, -0.05282), (-0.02803, 0.04609, -0.99854)36.48712, 30.46697, -40.72421
3given(-0.99927, 0.02157, 0.0314), (-0.02162, -0.99977, -0.00127), (0.03136, -0.00195, 0.99951)-43.46747, 18.55348, -70.37141
4given(0.93782, 0.3471, -0.0041), (0.34674, -0.93726, -0.03622), (-0.01641, 0.03255, -0.99934)-8.91992, 53.28581, -25.8986
5given(-0.99968, 0.01892, 0.01696), (-0.01884, -0.99981, 0.00455), (0.01705, 0.00423, 0.99985)-87.98461, 40.46713, -56.18718
6given(-0.99985, -0.01692, 0.0024), (-0.01693, 0.99985, -0.00407), (-0.00233, -0.00411, -0.99999)-42.07909, 23.59326, 101.84177
7given(0.93799, -0.34632, -0.01525), (0.34664, 0.93748, 0.03118), (0.0035, -0.03453, 0.9994)36.6148, 10.75115, 69.94672
8given(-0.99957, -0.01326, -0.02627), (-0.0133, 0.99991, 0.00145), (0.02625, 0.0018, -0.99965)-87.33016, 45.83342, 115.52911
9given(0.94069, -0.33926, 0.00287), (0.33856, 0.93924, 0.05658), (-0.02189, -0.05225, 0.99839)-7.31129, 33.4113, 85.1701
10given(1, -0.00128, -0.00257), (-0.00128, -1, -0.00085), (-0.00257, 0.00086, -1)45.33779, 63.94464, 44.79539
11given(-0.92799, 0.3723, -0.01517), (-0.3726, -0.92747, 0.03114), (-0.00248, 0.03455, 0.9994)-32.69117, 78.46609, 13.1007
12given(0.99936, 0.01139, -0.03395), (0.01174, -0.99988, 0.01011), (-0.03383, -0.0105, -0.99937)0.35277, 86.66576, 58.38307
13given(-0.93846, 0.34516, 0.01287), (-0.34397, -0.9373, 0.05614), (0.03144, 0.04826, 0.99834)-79.57493, 99.25872, 29.11652
14given(0.99967, -0.02, 0.01638), (0.02014, 0.99976, -0.0087), (-0.0162, 0.00902, 0.99983)44.55635, -23.03085, -14.29279
15given(-0.94035, -0.34022, 0.00033), (-0.33983, 0.93921, -0.04906), (0.01638, -0.04624, -0.9988)-34.93417, -35.06587, 16.24539

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Components

#1: Protein
GLUTATHIONE S-TRANSFERASE A3 / GLUTATHIONE-S-TRANSFERASE A3-3 / GST CLASS-ALPHA MEMBER 3


Mass: 25338.678 Da / Num. of mol.: 16
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: Q16772, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-ASD / 4-ANDROSTENE-3-17-DIONE


Mass: 286.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C19H26O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3263 / 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: 2.09 Å3/Da / Density % sol: 40.79 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.8
Details: HANGING VAPOUR DROP TECHIQUE 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 VAPOUR DROP TECHIQUE 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 25 MM ANDROSTENE DIONE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 17, 2006 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: THIN DIAMOND CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 338219 / % possible obs: 94.9 % / Observed criterion σ(I): 1.9 / Redundancy: 1.9 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.9 / % possible all: 93.6

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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 1TDI

1tdi


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.047 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 16208 5 %RANDOM
Rwork0.223 ---
obs0.225 304874 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å2-0.03 Å2-0.08 Å2
2---1.13 Å20.23 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28208 0 551 3263 32022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02229471
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3312.02739679
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.253488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48623.8451251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.642155720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.97615209
X-RAY DIFFRACTIONr_chiral_restr0.0840.24383
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0221601
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.215904
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.220049
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.23001
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.2155
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5031.518277
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.835228314
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.308312675
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0084.511353
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.364 1179
Rwork0.303 21923

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