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- PDB-3pgt: CRYSTAL STRUCTURE OF HGSTP1-1[I104] COMPLEXED WITH THE GSH CONJUG... -

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Basic information

Entry
Database: PDB / ID: 3pgt
TitleCRYSTAL STRUCTURE OF HGSTP1-1[I104] COMPLEXED WITH THE GSH CONJUGATE OF (+)-ANTI-BPDE
ComponentsPROTEIN (GLUTATHIONE S-TRANSFERASE)
KeywordsTRANSFERASE / PI CLASS / HGSTP1-1[I104] / DETOXIFICATION
Function / homology
Function and homology information


S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / negative regulation of smooth muscle cell chemotaxis / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / negative regulation of smooth muscle cell chemotaxis / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / response to L-ascorbic acid / linoleic acid metabolic process / Glutathione conjugation / nitric oxide binding / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / glutathione peroxidase activity / oligodendrocyte development / Paracetamol ADME / negative regulation of stress-activated MAPK cascade / negative regulation of JNK cascade / prostaglandin metabolic process / cellular response to glucocorticoid stimulus / negative regulation of interleukin-1 beta production / regulation of stress-activated MAPK cascade / Detoxification of Reactive Oxygen Species / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of vascular associated smooth muscle cell proliferation / glutathione transferase activity / protein serine/threonine kinase inhibitor activity / negative regulation of tumor necrosis factor production / animal organ regeneration / negative regulation of tumor necrosis factor-mediated signaling pathway / response to amino acid / toxic substance binding / regulation of ERK1 and ERK2 cascade / negative regulation of fibroblast proliferation / positive regulation of superoxide anion generation / negative regulation of MAPK cascade / negative regulation of canonical NF-kappaB signal transduction / glutathione metabolic process / xenobiotic metabolic process / cellular response to epidermal growth factor stimulus / fatty acid binding / central nervous system development / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of ERK1 and ERK2 cascade / cellular response to insulin stimulus / response to estradiol / cellular response to lipopolysaccharide / response to ethanol / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm / 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 / 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 / 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-GBX / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.14 Å
AuthorsJi, X. / Xiao, B.
Citation
Journal: Biochemistry / Year: 1999
Title: Structure and function of residue 104 and water molecules in the xenobiotic substrate-binding site in human glutathione S-transferase P1-1.
Authors: Ji, X. / Blaszczyk, J. / Xiao, B. / O'Donnell, R. / Hu, X. / Herzog, C. / Singh, S.V. / Zimniak, P.
#1: 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.
#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
DepositionMar 22, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Nov 13, 2019Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.6Sep 6, 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: PROTEIN (GLUTATHIONE S-TRANSFERASE)
B: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,42015
Polymers46,7562
Non-polymers2,66513
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-66 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.830, 89.710, 68.410
Angle α, β, γ (deg.)90.00, 97.76, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-789-

HOH

21A-790-

HOH

31A-791-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.933036, -0.14438, 0.329543), (-0.145495, -0.989127, -0.021419), (0.329052, -0.027962, -0.943898)
Vector: -4.54915, 2.98727, 27.73261)

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Components

#1: Protein PROTEIN (GLUTATHIONE S-TRANSFERASE) / GST / HGSTP1-1[I104]


Mass: 23377.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HGSTP1-1[I104] AND HGSTP1-1[V104] ARE NATURALLY OCCURRING VARIANTS OF HGSTP1-1
Source: (gene. exp.) Homo sapiens (human) / Strain: BL21 (DE3) PLYSS / Cellular location: CYTOPLASM / Gene: GTP_HUMAN / Organ: PLACENTA / 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.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GBX / 2-AMINO-4-[1-(CARBOXYMETHYL-CARBAMOYL)-2-(9-HYDROXY-7,8-DIOXO-7,8,9,10-TETRAHYDRO-BENZO[DEF]CHRYSEN-10-YLSULFANYL)-ETHYLCARBAMOYL]-BUTYRIC ACID / GLUTATHIONE CONJUGATE OF (+)-ANTI-BPDE


Mass: 605.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H27N3O9S
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.07 Å3/Da / Density % sol: 40 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.3 mMprotein1drop
250 mMMES1drop
30.5 mMGSBpd1drop
45 mMcobalt hexammine chloride1drop
50.9 Mammonium sulfate1drop
61.8 Mammonium sulfate1reservoir
710 mMcobaltic hexamine chloride1reservoir
80.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.14→20 Å / Num. obs: 23834 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 3.15 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 23.93
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 1.92 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 7.71 / % possible all: 83.2
Reflection
*PLUS
Redundancy: 8.61 %
Reflection shell
*PLUS
% possible obs: 83.2 %

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Processing

Software
NameClassification
X-PLORmodel building
SHELXLrefinement
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementStarting model: PDB ENTRY 1PGT

1pgt


Resolution: 2.14→20 Å / Num. parameters: 15785 / Num. restraintsaints: 14142 / Cross valid method: FREE R (AT EARLY STAGE) / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: X-PLOR WAS USED AT THE EARLY STAGE OF THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.159 --RANDOM
all0.1559 23832 --
obs0.1559 -92.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3942.5
Refinement stepCycle: LAST / Resolution: 2.14→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 169 491 3944
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.021
X-RAY DIFFRACTIONs_zero_chiral_vol0.026
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.032
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.072
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.155 / Rfactor Rwork: 0.1559
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.021
X-RAY DIFFRACTIONs_chiral_restr0.026

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