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- PDB-2gsr: Structure of porcine class pi glutathione s-transferase -

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Basic information

Entry
Database: PDB / ID: 2gsr
TitleStructure of porcine class pi glutathione s-transferase
ComponentsCLASS PI GST GLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


glutathione derivative biosynthetic process / hepoxilin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / mitochondrion / nucleus / cytosol
Similarity search - Function
Glutathione S-transferase, Pi 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 / 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, Pi 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 / 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
GLUTATHIONE SULFONIC ACID / Glutathione S-transferase P
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.11 Å
AuthorsReinemer, P. / Dirr, H.W. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Refined crystal structure of porcine class Pi glutathione S-transferase (pGST P1-1) at 2.1 A resolution.
Authors: Dirr, H. / Reinemer, P. / Huber, R.
#1: Journal: Embo J. / Year: 1991
Title: The Three-Dimensional Structure of Class Pi Glutathione S-Transferase in Complex with Glutathione Sulfonate at 2.3 A Resolution
Authors: Reinemer, P. / Dirr, H.W. / Ladenstein, R. / Schaffer, J. / Gallay, O. / Huber, R.
History
DepositionMar 21, 1996Processing site: BNL
SupersessionNov 8, 1996ID: 1GSR
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Apr 18, 2018Group: Advisory / Data collection / Other
Category: diffrn_detector / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.5Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CLASS PI GST GLUTATHIONE S-TRANSFERASE
B: CLASS PI GST GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7894
Polymers47,0782
Non-polymers7112
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.250, 82.530, 54.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.00633, 0.0146, 0.99987), (0.02097, -0.99967, 0.01473), (0.99976, 0.02107, 0.00602)
Vector: 37.248, 47.015, -37.956)

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Components

#1: Protein CLASS PI GST GLUTATHIONE S-TRANSFERASE / PI GST


Mass: 23539.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: LUNG / References: UniProt: P80031, glutathione transferase
#2: Chemical ChemComp-GTS / GLUTATHIONE SULFONIC ACID


Mass: 355.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O9S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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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 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 mg/mlprotein1drop
23 mMglutathione sulphonate1drop
316 %(w/v)PEG40001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.11 Å / Num. obs: 21669 / % possible obs: 81 % / Observed criterion σ(I): 2.5 / Rmerge(I) obs: 0.084 / Rsym value: 0.037
Reflection shellResolution: 2.11→2.21 Å / % possible all: 32
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 113811
Reflection shell
*PLUS
% possible obs: 32 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.11→8 Å /
RfactorNum. reflection
Rwork0.165 -
obs0.165 21165
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.11→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 46 254 3614
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_deg2.801
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.92
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.194
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.92
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.194
LS refinement shell
*PLUS
Highest resolution: 2.11 Å / Lowest resolution: 2.21 Å / Rfactor obs: 0.228

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