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- PDB-1ags: A SURFACE MUTANT (G82R) OF A HUMAN ALPHA-GLUTATHIONE S-TRANSFERAS... -

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Basic information

Entry
Database: PDB / ID: 1ags
TitleA SURFACE MUTANT (G82R) OF A HUMAN ALPHA-GLUTATHIONE S-TRANSFERASE SHOWS DECREASED THERMAL STABILITY AND A NEW MODE OF MOLECULAR ASSOCIATION IN THE CRYSTAL
ComponentsGLUTATHIONE S-TRANSFERASE ALPHA
KeywordsTRANSFERASE (GLUTATHIONE)
Function / homology
Function and homology information


Glutathione conjugation / Azathioprine ADME / glutathione transferase / glutathione transferase activity / glutathione metabolic process / epithelial cell differentiation / xenobiotic metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / 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, 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, 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, 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
S-HEXYLGLUTATHIONE / Glutathione S-transferase A2
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsZeng, K. / Rose, J.P. / Wang, B.C.
CitationJournal: Proteins / Year: 1994
Title: A surface mutant (G82R) of a human alpha-glutathione S-transferase shows decreased thermal stability and a new mode of molecular association in the crystal.
Authors: Zeng, K. / Rose, J.P. / Chen, H.C. / Strickland, C.L. / Tu, C.P. / Wang, B.C.
History
DepositionJan 23, 1995Processing site: BNL
Revision 1.0Jul 10, 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_ref_seq_dif / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE ALPHA
B: GLUTATHIONE S-TRANSFERASE ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1594
Polymers51,3742
Non-polymers7852
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.500, 92.900, 115.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE ALPHA / Coordinate model: Cα atoms only


Mass: 25687.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: PGTH121-G82R / Organ: LIVER / Plasmid: PKK223-3 / Gene (production host): PGTH121-G82R / Production host: Escherichia coli (E. coli) / References: UniProt: P09210, glutathione transferase
#2: Chemical ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30N3O6S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
225 mMTris-HCl1drop
318 %PEG33501reservoir
41 mMEDTA1reservoir
50.05 %(w/v)1,2,3-heptanetriol1reservoir
6100 mMTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 18098 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.0996
Reflection
*PLUS
Highest resolution: 2.5 Å / % possible obs: 92.6 % / Rmerge(I) obs: 0.0996

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
XENGENV. 2.1data reduction
X-PLORphasing
RefinementResolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.31 --
obs0.31 11851 86 %
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms442 0 52 0 494
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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