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- PDB-6gsw: FIRST-SPHERE AND SECOND-SPHERE ELECTROSTATIC EFFECTS IN THE ACTIV... -

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Basic information

Entry
Database: PDB / ID: 6gsw
TitleFIRST-SPHERE AND SECOND-SPHERE ELECTROSTATIC EFFECTS IN THE ACTIVE SITE OF A CLASS MU GLUTATHIONE TRANSFERASE
ComponentsMU CLASS GLUTATHIONE S-TRANSFERASE OF ISOENZYME 3-3
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE / ISOENZYME 3-3 / T13V MUTANT
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 / xenobiotic catabolic process / response to axon injury / 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 / cytoplasm / cytosol
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-GPS / Glutathione S-transferase Mu 1
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsXiao, G. / Ji, X. / Armstrong, R.N. / Gilliland, G.L.
Citation
Journal: Biochemistry / Year: 1996
Title: First-sphere and second-sphere electrostatic effects in the active site of a class mu gluthathione transferase.
Authors: Xiao, G. / Liu, S. / Ji, X. / Johnson, W.W. / Chen, J. / Parsons, J.F. / Stevens, W.J. / Gilliland, G.L. / Armstrong, R.N.
#1: 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.
#2: 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.
#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.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.
#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.
History
DepositionJan 26, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...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
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,9257
Polymers51,6342
Non-polymers1,2915
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-60 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.530, 69.280, 81.410
Angle α, β, γ (deg.)90.00, 105.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-389-

HOH

21B-339-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8204, -0.10958, 0.5612), (-0.11259, -0.99321, -0.02935), (0.5606, -0.03911, -0.82716)
Vector: -6.19904, 31.85858, 26.61017)

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Components

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


Mass: 25816.816 Da / Num. of mol.: 2 / Mutation: T13V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / Gene: CDNA INSERT OF CLONE PGT33MX / Organ: LIVER / Plasmid: PGT33MXT13V / Gene (production host): CDNA INSERT OF CLONE PGT33MX / Production host: Escherichia coli (E. coli) / Strain (production host): M5219 / References: UniProt: P04905, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GPS / L-gamma-glutamyl-S-[(9S,10S)-10-hydroxy-9,10-dihydrophenanthren-9-yl]-L-cysteinylglycine


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


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.33 Å3/Da / Density % sol: 47 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-12 mg/mlprotein1drop
225 mMTris-HCl1drop
31 mMEDTA1drop
40.2 %beta-octyl D-glucopyranoside1drop
52 mMproduct inhibitor1drop
640-50 %satammonium sulfate1drop
760-72 %satammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 16, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 40544 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 3.64 % / Rmerge(I) obs: 0.09
Reflection
*PLUS
Num. obs: 37279 / Num. measured all: 135610 / Rmerge(I) obs: 0.066

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Processing

Software
NameClassification
GPRLSArefinement
XENGENdata reduction
XENGENdata scaling
RefinementResolution: 1.85→6 Å / σ(F): 4
RfactorNum. reflection% reflection
Rwork0.163 --
obs-32948 84.2 %
Displacement parametersBiso mean: 16.87 Å2
Refinement stepCycle: LAST / Resolution: 1.85→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3636 0 85 324 4045
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0360.042
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8511
X-RAY DIFFRACTIONp_mcangle_it1.361.5
X-RAY DIFFRACTIONp_scbond_it1.6471.5
X-RAY DIFFRACTIONp_scangle_it2.5212
X-RAY DIFFRACTIONp_plane_restr0.0220.03
X-RAY DIFFRACTIONp_chiral_restr0.2060.2
X-RAY DIFFRACTIONp_singtor_nbd0.1920.3
X-RAY DIFFRACTIONp_multtor_nbd0.1730.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1490.3
X-RAY DIFFRACTIONp_planar_tor5.35
X-RAY DIFFRACTIONp_staggered_tor17.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor17.715
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: GPRLSA / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS

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