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- PDB-2pgt: CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE S-TRANSFERASE P1-1[V104] C... -

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Entry
Database: PDB / ID: 2pgt
TitleCRYSTAL STRUCTURE OF HUMAN GLUTATHIONE S-TRANSFERASE P1-1[V104] COMPLEXED WITH (9R,10R)-9-(S-GLUTATHIONYL)-10-HYDROXY-9,10-DIHYDROPHENANTHRENE
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / PI CLASS / HGSTP1-1[V104] / DETOXIFICATION
Function / homology
Function and homology information


S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / kinase regulator activity / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of JUN kinase activity ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / kinase regulator activity / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of JUN kinase activity / linoleic acid metabolic process / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / nitric oxide binding / JUN kinase binding / glutathione peroxidase activity / Paracetamol ADME / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / prostaglandin metabolic process / regulation of stress-activated MAPK cascade / Detoxification of Reactive Oxygen Species / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of tumor necrosis factor production / glutathione transferase activity / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of MAP kinase activity / negative regulation of MAPK cascade / regulation of ERK1 and ERK2 cascade / negative regulation of fibroblast proliferation / negative regulation of canonical NF-kappaB signal transduction / glutathione metabolic process / xenobiotic metabolic process / positive regulation of superoxide anion generation / central nervous system development / fatty acid binding / negative regulation of protein kinase activity / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of ERK1 and ERK2 cascade / cellular response to lipopolysaccharide / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm
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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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, Pi class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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 P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.9 Å
AuthorsJi, X.
Citation
Journal: Biochemistry / Year: 1997
Title: Structure and function of the xenobiotic substrate-binding site and location of a potential non-substrate-binding site in a class pi glutathione S-transferase.
Authors: Ji, X. / Tordova, M. / O'Donnell, R. / Parsons, J.F. / Hayden, J.B. / Gilliland, G.L. / Zimniak, P.
#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: Eur.J.Biochem. / Year: 1994
Title: Naturally Occurring Human Glutathione S-Transferase Gstp1-1 Isoforms with Isoleucine and Valine in Position 104 Differ in Enzymic Properties
Authors: Zimniak, P. / Nanduri, B. / Pikula, S. / Bandorowicz-Pikula, J. / Singhal, S.S. / Srivastava, S.K. / Awasthi, S. / Awasthi, Y.C.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Three-Dimensional Structure of Class Pi Glutathione S-Transferase from Human Placenta in Complex with S-Hexylglutathione at 2.8 A Resolution
Authors: Reinemer, P. / Dirr, H.W. / Ladenstein, R. / Huber, R. / Lo Bello, M. / Federici, G. / Parker, M.W.
History
DepositionFeb 17, 1997Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3037
Polymers46,7272
Non-polymers1,5765
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-36 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.180, 90.540, 69.370
Angle α, β, γ (deg.)90.00, 98.45, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.940109, -0.104945, 0.324317), (-0.102554, -0.994426, -0.024505), (0.325081, -0.010223, -0.945631)
Vector: -4.70443, 1.28775, 27.94591)

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE / GST / HGSTP1-1[V104]


Mass: 23363.742 Da / Num. of mol.: 2 / Mutation: VAL 104 VARIANT
Source method: isolated from a genetically manipulated source
Details: HGSTP1-1[V104] AND HGSTP1-1[I104] ARE NATURALLY OCCURRING VARIANTS OF HGSTP1-1 OBTAINED BY SITE-DIRECTED MUTAGENESIS
Source: (gene. exp.) Homo sapiens (human) / Cell line: 293 / Cellular location: CYTOPLASM / Gene: GTP_HUMAN / Organ: PLACENTA / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P09211, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 5.9 MG/ML PROTEIN IN 0.1 M HEPES BUFFER (PH 7.0) CONTAINING 8.3 MM S-HEXYLGLUTATHIONE AND 1.0 M BUFFERED (PH 7.0) AMMONIUM ...Details: CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 5.9 MG/ML PROTEIN IN 0.1 M HEPES BUFFER (PH 7.0) CONTAINING 8.3 MM S-HEXYLGLUTATHIONE AND 1.0 M BUFFERED (PH 7.0) AMMONIUM SULFATE. THE DROPS WERE EQUILIBRATED AT 293 K AGAINST WELL SOLUTION CONTAINING BETWEEN 1.9 - 2.0 M AMMONIUM SULFATE IN 0.1 M HEPES BUFFER (PH 7.0)., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.9 mg/mlprotein1drop
20.1 MHEPES1drop
38.3 mMGSHex1drop
41.0 Mammonium sulfate1drop
51.9-2.0 Mammonium sulfate1reservoir
60.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 40456 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 23.61 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.31
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1.45 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 1.77 / % possible all: 77.3
Reflection shell
*PLUS
% possible obs: 77.3 %

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Processing

Software
NameClassification
X-PLORmodel building
GPRLSArefinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1PGT

1pgt


Resolution: 1.9→6 Å / Cross valid method: THROUGHOUT / σ(F): 3
Details: X-PLOR IS USED AT EARLY STAGE OF REFINEMENT. GPRLSA IS A MODIFIED VERSION OF PROLSQ BY FUREY, WANG AND SAX (J. APPL. CRYSTALLOGR.,1982,15,160-166). CROSS-VALIDATION INCLUDES GEOMETRY CHECK ...Details: X-PLOR IS USED AT EARLY STAGE OF REFINEMENT. GPRLSA IS A MODIFIED VERSION OF PROLSQ BY FUREY, WANG AND SAX (J. APPL. CRYSTALLOGR.,1982,15,160-166). CROSS-VALIDATION INCLUDES GEOMETRY CHECK AND R FACTOR CALCULATION FOR ALL DATA.
RfactorNum. reflection% reflection
Rwork0.183 --
all-40456 -
obs-30838 83 %
Displacement parametersBiso mean: 26.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 100 344 3726
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0340.036
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0720.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7261
X-RAY DIFFRACTIONp_mcangle_it1.2251.5
X-RAY DIFFRACTIONp_scbond_it1.2981.5
X-RAY DIFFRACTIONp_scangle_it1.9952
X-RAY DIFFRACTIONp_plane_restr0.0230.03
X-RAY DIFFRACTIONp_chiral_restr0.1830.2
X-RAY DIFFRACTIONp_singtor_nbd0.2240.3
X-RAY DIFFRACTIONp_multtor_nbd0.1760.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2170.3
X-RAY DIFFRACTIONp_planar_tor6.95
X-RAY DIFFRACTIONp_staggered_tor18.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor17.915
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: GPRLSA / Classification: refinement
Refinement
*PLUS
σ(I): 1.5 / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

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