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- PDB-1guh: Structure determination and refinement of human alpha class gluta... -

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Basic information

Entry
Database: PDB / ID: 1guh
TitleStructure determination and refinement of human alpha class glutathione transferase A1-1, and a comparison with the MU and PI class enzymes
ComponentsGLUTATHIONE S-TRANSFERASE A1-1
KeywordsTRANSFERASE / glutathione transferase
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / linoleic acid metabolic process / steroid Delta-isomerase activity / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / linoleic acid metabolic process / steroid Delta-isomerase activity / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / epithelial cell differentiation / glutathione metabolic process / 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 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. ...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 / 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
S-BENZYL-GLUTATHIONE / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsSinning, I. / Kleywegt, G.J. / Jones, T.A.
CitationJournal: 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 enzymes.
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
DepositionFeb 24, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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 S-TRANSFERASE A1-1
B: GLUTATHIONE S-TRANSFERASE A1-1
C: GLUTATHIONE S-TRANSFERASE A1-1
D: GLUTATHIONE S-TRANSFERASE A1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7458
Polymers102,1564
Non-polymers1,5904
Water00
1
A: GLUTATHIONE S-TRANSFERASE A1-1
B: GLUTATHIONE S-TRANSFERASE A1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8734
Polymers51,0782
Non-polymers7952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-21 kcal/mol
Surface area19730 Å2
MethodPISA
2
C: GLUTATHIONE S-TRANSFERASE A1-1
D: GLUTATHIONE S-TRANSFERASE A1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8734
Polymers51,0782
Non-polymers7952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-22 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.800, 95.400, 105.200
Angle α, β, γ (deg.)90.00, 92.40, 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
Matrix: (-0.59723, 0.10833, 0.79472), (0.01811, -0.98876, 0.1484), (0.80187, 0.10302, 0.58895)
Vector: 104.88689, 37.31765, -4.50918)

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Components

#1: Protein
GLUTATHIONE S-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) / References: UniProt: P08263, glutathione transferase
#2: Chemical
ChemComp-GSB / S-BENZYL-GLUTATHIONE


Mass: 397.446 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H23N3O6S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 208.369-370 1989
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
235 mg/mlprotein1drop
32.5 mMligand1drop
450 mMbistrispropane1drop
51 %(v/v)2-mercaptoethanol1drop
620 %(w/v)PEG20001drop
750 mMbistrispropane1reservoir
81 %(v/v)2-mercaptoethanol1reservoir
920 %(w/v)PEG20001reservoir
1enzyme1drop0.005ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 25135 / Num. measured all: 46733 / Rmerge(I) obs: 0.053

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.229 / Rfactor obs: 0.229 / Highest resolution: 2.6 Å
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7184 0 108 0 7292
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 7.5 Å / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_dihedral_angle_d1
X-RAY DIFFRACTIONx_dihedral_angle_deg

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