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- PDB-3fyg: CRYSTAL STRUCTURE OF TETRADECA-(3-FLUOROTYROSYL)-GLUTATHIONE S-TR... -

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Basic information

Entry
Database: PDB / ID: 3fyg
TitleCRYSTAL STRUCTURE OF TETRADECA-(3-FLUOROTYROSYL)-GLUTATHIONE S-TRANSFERASE
ComponentsMU CLASS TETRADECA-(3-FLUOROTYROSYL)-GLUTATHIONE S-TRANSFERASE OF ISOENZYME
KeywordsTRANSFERASE / 3-FLUOROTYROSINE / UNNATURAL AMINO ACID / THREE-DIMENSIONAL STRUCTURE / DETOXIFICATION ENZYME
Function / homology
Function and homology information


Glutathione conjugation / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / response to metal ion / prostaglandin metabolic process / nickel cation binding / glutathione transferase ...Glutathione conjugation / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / response to metal ion / prostaglandin metabolic process / nickel cation binding / glutathione transferase / glutathione transferase activity / response to axon injury / response to amino acid / xenobiotic catabolic process / steroid binding / glutathione metabolic process / response to lead ion / sensory perception of smell / cellular response to xenobiotic stimulus / response to ethanol / response to xenobiotic stimulus / protein kinase binding / enzyme binding / protein homodimerization activity / protein-containing complex / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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, Mu class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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
Chem-GPR / Glutathione S-transferase Mu 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXiao, G. / Parsons, J.F. / Armstrong, R.N. / Gilliland, G.L.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Conformational changes in the crystal structure of rat glutathione transferase M1-1 with global substitution of 3-fluorotyrosine for tyrosine.
Authors: Xiao, G. / Parsons, J.F. / Tesh, K. / Armstrong, R.N. / Gilliland, G.L.
#1: Journal: J.Am.Chem.Soc. / Year: 1996
Title: Proton Configuration in the Ground State and Transition State of a Glutathione Transferase-Catalyzed Reaction Inferred from the Properties of Tetradeca(3-Fluorotyrosyl)Glutathione Transferase
Authors: Parsons, J.F. / Armstrong, R.N.
#2: Journal: Biochemistry / Year: 1994
Title: Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferase as Revealed by X-Ray Crystallographic Analysis of Product Complexes with the Diastereomers of 9- ...Title: Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferase as Revealed by X-Ray Crystallographic Analysis of Product Complexes with the Diastereomers of 9-(S-Glutathionyl)-10-Hydroxy-9,10-Dihydrophenanthrene
Authors: Ji, X. / Johnson, W.W. / Sesay, M.A. / Dickert, L. / Prasad, S.M. / Ammon, H.L. / Armstrong, R.N. / Gilliland, G.L.
#3: Journal: Biochemistry / Year: 1993
Title: Snapshots Along the Reaction Coordinate of an Snar Reaction Catalyzed by Glutathione Transferase
Authors: Ji, X. / Armstrong, R.N. / Gilliland, G.L.
#4: Journal: J.Am.Chem.Soc. / Year: 1993
Title: Second-Sphere Electrostatic Effects in the Active Site of Glutathione S-Transferase. Observation of an on-Facet Hydrogen Bond between the Side Chain of Threonine 13 and the Pi-Cloud of ...Title: Second-Sphere Electrostatic Effects in the Active Site of Glutathione S-Transferase. Observation of an on-Facet Hydrogen Bond between the Side Chain of Threonine 13 and the Pi-Cloud of Tyrosine 6 and its Influence on Catalysis
Authors: Liu, S. / Ji, X. / Gilliland, G.L. / Stevens, W.J. / Armstrong, R.N.
#5: Journal: Biochemistry / Year: 1992
Title: The Three-Dimensional Structure of a Glutathione S-Transferase from the Mu Gene Class. Structural Analysis of the Binary Complex of Isoenzyme 3-3 and Glutathione at 2.2-A Resolution
Authors: Ji, X. / Zhang, P. / Armstrong, R.N. / Gilliland, G.L.
#6: Journal: J.Biol.Chem. / Year: 1992
Title: Contribution of Tyrosine 6 to the Catalytic Mechanism of Isoenzyme 3-3 of Glutathione S-Transferase
Authors: Liu, S. / Zhang, P. / Ji, X. / Johnson, W.W. / Gilliland, G.L. / Armstrong, R.N.
History
DepositionAug 7, 1997Processing site: BNL
Revision 1.0Jun 1, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MU CLASS TETRADECA-(3-FLUOROTYROSYL)-GLUTATHIONE S-TRANSFERASE OF ISOENZYME
B: MU CLASS TETRADECA-(3-FLUOROTYROSYL)-GLUTATHIONE S-TRANSFERASE OF ISOENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1084
Polymers52,1052
Non-polymers1,0032
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-26 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.430, 88.420, 57.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.28207, -0.74774, -0.6011), (-0.7546, -0.214, 0.62031), (-0.59247, 0.62856, -0.50388)
Vector: 49.75153, 29.32965, 22.56671)

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Components

#1: Protein MU CLASS TETRADECA-(3-FLUOROTYROSYL)-GLUTATHIONE S-TRANSFERASE OF ISOENZYME / RAT GST


Mass: 26052.660 Da / Num. of mol.: 2
Mutation: MANY TYROSINES MUTATED INTO 3-FLUOROTYROSINE. CHAIN A, B, Y6YOF, Y22OFY, Y27YOF, Y32YOF, Y40YOF, Y61YOF, Y78YOF, Y115YOF Y137OFY, Y154YOF, Y160YOF, Y166OFY, Y196YOF, Y202YOF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Gene: CDNA INSERT OF CLONE PGT33M / Organ: LIVER / Plasmid: PSW1GST33 / Species (production host): Escherichia coli / Gene (production host): CDNA INSERT OF CLONE PGT33M / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04905, glutathione transferase
#2: Chemical ChemComp-GPR / (9R,10R)-9-(S-GLUTATHIONYL)-10-HYDROXY-9,10-DIHYDROPHENANTHRENE


Mass: 501.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27N3O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22 mMproduct1drop
30.3 %n-octyl beta-D-glucopyranoside1drop
410 %PEG30001drop
51 M1dropLiCl
622-26 %PEG30001reservoir
71 M1reservoirLiCl
850 mMMOPS1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1996
RadiationMonochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→65 Å / Num. obs: 22702 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.75 % / Biso Wilson estimate: 39.8 Å2 / Rsym value: 0.075 / Net I/σ(I): 9.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4 / Rsym value: 0.35 / % possible all: 80
Reflection
*PLUS
Num. measured all: 243942 / Rmerge(I) obs: 0.083

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GST: CLASS MU GST

3gst


Resolution: 2.2→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 2.2 / Stereochemistry target values: TNT PROTGEO /
RfactorNum. reflection% reflection
obs0.17 243942 99.9 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 220 Å2 / ksol: 0.81 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 70 431 4155
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01538520.8
X-RAY DIFFRACTIONt_angle_deg2.3651721.3
X-RAY DIFFRACTIONt_dihedral_angle_d2022900
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011082
X-RAY DIFFRACTIONt_gen_planes0.0115325
X-RAY DIFFRACTIONt_it5.8135401
X-RAY DIFFRACTIONt_nbd0.0914310
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg200
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_improper_angle_deg0.01
X-RAY DIFFRACTIONt_plane_restr0.015

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