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- PDB-5fwg: TETRA-(5-FLUOROTRYPTOPHANYL)-GLUTATHIONE TRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 5fwg
TitleTETRA-(5-FLUOROTRYPTOPHANYL)-GLUTATHIONE TRANSFERASE
ComponentsTETRA-(5-FLUOROTRYPTOPHANYL)-GLUTATHIONE TRANSFERASE MU CLASS
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE / UNNATURAL AMINO ACID / 5-FLUOROTRYPTOPHAN / THREE-DIMENSIONAL STRUCTURE
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 amino acid / response to axon injury / xenobiotic catabolic process / steroid binding / glutathione metabolic process / response to lead ion / cellular response to xenobiotic stimulus / sensory perception of smell / response to ethanol / protein kinase binding / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / 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 MODIFICATION / Resolution: 2 Å
AuthorsParsons, J.F. / Xiao, G. / Armstrong, R.N. / Gilliland, G.L.
Citation
Journal: Biochemistry / Year: 1998
Title: Enzymes harboring unnatural amino acids: mechanistic and structural analysis of the enhanced catalytic activity of a glutathione transferase containing 5-fluorotryptophan.
Authors: Parsons, J.F. / Xiao, G. / Gilliland, G.L. / Armstrong, R.N.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Tyrosine 115 Participates Both in Chemical and Physical Steps of the Catalytic Mechanism of a Glutathione S-Transferase
Authors: Johnson, W.W. / Liu, S. / Ji, X. / Gilliland, G.L. / Armstrong, R.N.
#2: 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.
#3: 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.
History
DepositionNov 8, 1997Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TETRA-(5-FLUOROTRYPTOPHANYL)-GLUTATHIONE TRANSFERASE MU CLASS
B: TETRA-(5-FLUOROTRYPTOPHANYL)-GLUTATHIONE TRANSFERASE MU CLASS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7854
Polymers51,7822
Non-polymers1,0032
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-22 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.939, 68.747, 80.539
Angle α, β, γ (deg.)90.00, 105.08, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.841869, -0.090312, 0.532071), (-0.089096, -0.995629, -0.028023), (0.532277, -0.023813, -0.846236)
Vector: -6.461, 31.394, 27.26)

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Components

#1: Protein TETRA-(5-FLUOROTRYPTOPHANYL)-GLUTATHIONE TRANSFERASE MU CLASS / RAT MU CLASS GST / RAT M1-1 GST


Mass: 25890.756 Da / Num. of mol.: 2 / Mutation: 4 TRYPTOPHANS MUTATED TO 5-FLUOROTRYPTOPHANS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Gene: CDNA INSERT OF 3-3 (M1-1) ENZY / Organ: LIVER / Plasmid: PSW1GST33 / Species (production host): Escherichia coli / Gene (production host): CDNA INSERT OF 3-3 (M1-1) ENZYME / 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.: 371 / 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: 2.31 Å3/Da / Density % sol: 47 %
Crystal growpH: 7.6 / Details: pH 7.6
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
22 mMinhibitor1drop
30.3 %n-octyl-beta-D-glycopyranoside1drop
410 %PEG30001drop
5100 mMHEPES1drop
624 %PEG30001reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 8, 1997 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→65 Å / Num. obs: 184888 / % possible obs: 94.9 % / Observed criterion σ(I): 5 / Redundancy: 6.24 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 15 / % possible all: 68.3
Reflection
*PLUS
Num. obs: 29587 / % possible obs: 95 % / Num. measured all: 184888
Reflection shell
*PLUS
% possible obs: 68.3 % / Mean I/σ(I) obs: 9.1

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Processing

Software
NameVersionClassification
X-PLORmodel building
TNT5Erefinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR MODIFICATION
Starting model: PDB ENTRY 3GST

3gst


Resolution: 2→65 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 2 / Stereochemistry target values: TNT PROTGEO /
RfactorNum. reflection% reflection
obs0.18 28281 90 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 71.4 Å2 / ksol: 0.814 e/Å3
Refinement stepCycle: LAST / Resolution: 2→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 70 371 4085
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01738560.8
X-RAY DIFFRACTIONt_angle_deg351541.2
X-RAY DIFFRACTIONt_dihedral_angle_d19.5322960
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0131121.5
X-RAY DIFFRACTIONt_gen_planes0.0165344
X-RAY DIFFRACTIONt_it7.08937021
X-RAY DIFFRACTIONt_nbd0.02315410
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 28444 / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.022
X-RAY DIFFRACTIONt_angle_deg3.03
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.530
X-RAY DIFFRACTIONt_plane_restr0.02

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