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- PDB-1gsf: GLUTATHIONE TRANSFERASE A1-1 COMPLEXED WITH ETHACRYNIC ACID -

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Basic information

Entry
Database: PDB / ID: 1gsf
TitleGLUTATHIONE TRANSFERASE A1-1 COMPLEXED WITH ETHACRYNIC ACID
ComponentsGLUTATHIONE TRANSFERASE A1-1
KeywordsTRANSFERASE (GLUTATHIONE) / A1-1
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / NFE2L2 regulating anti-oxidant/detoxification enzymes ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / epithelial cell differentiation / xenobiotic metabolic process / fatty acid binding / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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
ETHACRYNIC ACID / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsL'Hermite, G. / Sinning, I. / Cameron, A.D. / Jones, T.A.
Citation
Journal: Structure / Year: 1995
Title: Structural analysis of human alpha-class glutathione transferase A1-1 in the apo-form and in complexes with ethacrynic acid and its glutathione conjugate.
Authors: Cameron, A.D. / Sinning, I. / L'Hermite, G. / Olin, B. / Board, P.G. / Mannervik, B. / Jones, T.A.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Structure Determination and Refinement of Human Alpha Class Glutathione Transferase A1-1, and a Comparison with the Mu and Pi Class Enzyme
Authors: Sinning, I. / Kleywegt, G.J. / Cowan, S.W. / Reinemer, P. / Dirr, H.W. / Huber, R. / Gilliland, G.L. / Armstrong, R.N. / Ji, X. / Board, P.G. / Olin, B. / Mannervik, B. / Jones, T.A.
History
DepositionJun 9, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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 TRANSFERASE A1-1
B: GLUTATHIONE TRANSFERASE A1-1
C: GLUTATHIONE TRANSFERASE A1-1
D: GLUTATHIONE TRANSFERASE A1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3688
Polymers102,1564
Non-polymers1,2134
Water2,702150
1
A: GLUTATHIONE TRANSFERASE A1-1
B: GLUTATHIONE TRANSFERASE A1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6844
Polymers51,0782
Non-polymers6062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-22 kcal/mol
Surface area20310 Å2
MethodPISA
2
C: GLUTATHIONE TRANSFERASE A1-1
D: GLUTATHIONE TRANSFERASE A1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6844
Polymers51,0782
Non-polymers6062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-22 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.800, 95.600, 105.300
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO A 56 / 2: CIS PROLINE - PRO B 56
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.59237, 0.10246, 0.79912), (0.00376, -0.99152, 0.12992), (0.80566, 0.07997, 0.58696)105.18658, 38.57485, -4.56058
2given(-0.58756, 0.10534, 0.8023), (0.00078, -0.99142, 0.13074), (0.80918, 0.07745, 0.58243)104.87399, 38.83441, -4.58805
3given(-0.57171, -0.02076, 0.82019), (-0.01954, -0.99905, -0.03891), (0.82022, -0.03827, 0.57076)108.05824, 41.26085, -55.51672
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 2 .. A 438 TRANSFORMS A CHAIN OF DIMER TO A CHAIN OF SECOND DIMER OF THE ASYMMETRIC UNIT M2 B 2 .. B 438 TRANSFORMS B CHAIN OF DIMER TO B CHAIN OF SECOND DIMER OF THE ASYMMETRIC UNIT M3 A 2 .. A 438 B 2 .. B 438 0.001 TRANSFORMS A CHAIN OF DIMER TO B CHAIN OF DIMER

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Components

#1: Protein
GLUTATHIONE TRANSFERASE A1-1


Mass: 25538.924 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PTACGST2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM103 / References: UniProt: P08263, glutathione transferase
#2: Chemical
ChemComp-EAA / ETHACRYNIC ACID / Etacrynic acid


Mass: 303.138 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H12Cl2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES ARE NUMBERED FROM 2 TO 222. THE ETHACRYNIC ACID HAS BEEN NUMBERED 223.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
155 mg/mlprotein1drop
210-20 %PEG20001drop
3100 mMTris-HCl1drop
430 mMNaAc1drop
51 %beta-mercaptoethanol1drop
610-20 %PEG20001reservoir
7100 mMTris-HCl1reservoir
830 mMNaAc1reservoir
91 %beta-mercaptoethanol1reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 21, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 26072 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.078
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. measured all: 41606 / Rmerge(I) obs: 0.078

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
RefinementResolution: 2.7→7.5 Å / σ(F): 0
Details: RESIDUE ARG 89 HAS BEEN MODELLED IN 2 CONFORMATIONS AS FOR THE HIGHER RESOLUTION GST A 1-1 STRUCTURE COMPLEXED WITH A GLUTATHIONE, ETHACRYNIC ACID CONJUGATE. THIS RESIDUE LIES AT THE DIMER ...Details: RESIDUE ARG 89 HAS BEEN MODELLED IN 2 CONFORMATIONS AS FOR THE HIGHER RESOLUTION GST A 1-1 STRUCTURE COMPLEXED WITH A GLUTATHIONE, ETHACRYNIC ACID CONJUGATE. THIS RESIDUE LIES AT THE DIMER INTERFACE CLOSE TO AN NCS COPY OF ITSELF.
RfactorNum. reflection% reflection
Rfree0.261 -5 %
Rwork0.229 --
obs0.229 24937 94.9 %
Displacement parametersBiso mean: 43 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.7→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7228 0 76 150 7454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.46
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.31
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.31

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