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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


Glutathione conjugation / Isomerases, Intramolecular oxidoreductases, Transposing C=C bonds / linoleic acid metabolic process / prostaglandin metabolic process / steroid delta-isomerase activity / Oxidoreductases, Acting on a peroxide as acceptor, Peroxidases / glutathione derivative biosynthetic process / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity ...Glutathione conjugation / Isomerases, Intramolecular oxidoreductases, Transposing C=C bonds / linoleic acid metabolic process / prostaglandin metabolic process / steroid delta-isomerase activity / Oxidoreductases, Acting on a peroxide as acceptor, Peroxidases / glutathione derivative biosynthetic process / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / epithelial cell differentiation / xenobiotic metabolic process / extracellular exosome / cytosol
Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal / Glutathione S-transferase, alpha class / Thioredoxin-like superfamily / Glutathione S-transferase, C-terminal domain superfamily / Glutathione Transferase family / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase N-terminal domain profile. / Soluble glutathione S-transferase C-terminal domain profile.
Glutathione S-transferase A1
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 9, 1995-
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
γ
α
β
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:

Code: given

IDMatrixVector
1(-0.59237, 0.10246, 0.79912), (0.00376, -0.99152, 0.12992), (0.80566, 0.07997, 0.58696)105.18658, 38.57485, -4.56058
2(-0.58756, 0.10534, 0.8023), (0.00078, -0.99142, 0.13074), (0.80918, 0.07745, 0.58243)104.87399, 38.83441, -4.58805
3(-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/peptide
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


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


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O / Water
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

Crystal-ID: 1

IDConc.Common nameSol-ID
155 mg/mlproteindrop
210-20 %PEG2000drop
3100 mMTris-HCldrop
430 mMNaAcdrop
51 %beta-mercaptoethanoldrop
610-20 %PEG2000reservoir
7100 mMTris-HClreservoir
830 mMNaAcreservoir
91 %beta-mercaptoethanolreservoir

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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 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
Refinement-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
Refinement-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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