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- PDB-6y1e: Crystal structure of human glutathione transferase P1-1 (hGSTP1-1... -

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Basic information

Entry
Database: PDB / ID: 6y1e
TitleCrystal structure of human glutathione transferase P1-1 (hGSTP1-1) that was co-crystallised in the presence of indanyloxyacetic acid-94 (IAA-94)
ComponentsGlutathione S-transferase P
KeywordsTRANSFERASE / Indanyloxyacetic acid-94 / IAA-94 / chloride ion channel inhibitor / ethacrynic acid / EA / glutathione transferase P1-1 / CLIC1
Function / homology
Function and homology information


S-nitrosoglutathione binding / nitric oxide storage / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of leukocyte proliferation / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of leukocyte proliferation / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / nitric oxide binding / linoleic acid metabolic process / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / Paracetamol ADME / JUN kinase binding / glutathione peroxidase activity / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / negative regulation of MAPK cascade / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / 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 canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / glutathione metabolic process / xenobiotic metabolic process / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / central nervous system development / response to reactive oxygen species / fatty acid binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / secretory granule lumen / vesicle / cellular response to lipopolysaccharide / 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 Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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
GLUTATHIONE / Chem-O7Z / TRIETHYLENE GLYCOL / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.402 Å
AuthorsPandian, R. / Worth, R. / Thangaraj, V. / Sayed, Y. / Dirr, H.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Science and Technology Funding CouncilST/R002754/1 United Kingdom
CitationJournal: To Be Published
Title: The interaction of IAA-94 with the soluble conformation of the CLIC1 protein and its structural homolog hGSTP1-1
Authors: Worth, R. / Pandian, R. / Thangaraj, V. / Sayed, Y. / Dirr, H.W.
History
DepositionFeb 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase P
B: Glutathione S-transferase P
C: Glutathione S-transferase P
D: Glutathione S-transferase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,28419
Polymers93,5114
Non-polymers3,77315
Water15,151841
1
A: Glutathione S-transferase P
B: Glutathione S-transferase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6709
Polymers46,7562
Non-polymers1,9157
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-15 kcal/mol
Surface area17820 Å2
MethodPISA
2
D: Glutathione S-transferase P
hetero molecules

C: Glutathione S-transferase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,61310
Polymers46,7562
Non-polymers1,8588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area5270 Å2
ΔGint-6 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.638, 72.179, 88.624
Angle α, β, γ (deg.)90.000, 90.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glutathione S-transferase P / GST class-pi / GSTP1-1


Mass: 23377.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTP1, FAEES3, GST3 / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase

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Non-polymers , 5 types, 856 molecules

#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-O7Z / 2-[[6,7-bis(chloranyl)-2-cyclopentyl-2-methyl-1-oxidanylidene-3~{H}-inden-5-yl]oxy]ethanoic acid / indanyloxyacetic acid-94 / IAA-94


Mass: 357.228 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C17H18Cl2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 841 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.61 % / Description: Cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mg/ml hGSTP1-1 (50 mM dipotassium phosphate, 1.5 mM EDTA, 10 mM DTT, 10 mM GSH and 0.02 % (w/v) sodium azide, pH 7.0) with 3.5 mM IAA-94 (5% DMSO (v/v)) was crystallized in 100 mM MES and ...Details: 10 mg/ml hGSTP1-1 (50 mM dipotassium phosphate, 1.5 mM EDTA, 10 mM DTT, 10 mM GSH and 0.02 % (w/v) sodium azide, pH 7.0) with 3.5 mM IAA-94 (5% DMSO (v/v)) was crystallized in 100 mM MES and 16 % (w/v) PEG-6000, pH 6.5. The crystals were harvested and then immersed two to three times in 100% (v/v) Parabar 10312 (Paratone)
PH range: 6.5 - 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.916 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.402→68.638 Å / Num. obs: 163749 / % possible obs: 96.8 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.142 / Net I/σ(I): 7.1
Reflection shellResolution: 1.402→1.427 Å / Redundancy: 4.7 % / Rmerge(I) obs: 2.251 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 7637 / CC1/2: 0.327 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AQX

1aqx


Resolution: 1.402→55.966 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.94
RfactorNum. reflection% reflection
Rfree0.2511 7888 4.91 %
Rwork0.2166 --
obs0.2183 160658 95.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.24 Å2 / Biso mean: 22.178 Å2 / Biso min: 8.09 Å2
Refinement stepCycle: final / Resolution: 1.402→55.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6545 0 187 841 7573
Biso mean--28.25 32.18 -
Num. residues----835
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4024-1.41840.43182260.454380672
1.4184-1.4350.4412210.4481399275
1.435-1.45250.4291960.433395374
1.4525-1.47090.43392840.4138476590
1.4709-1.49030.39312600.386510096
1.4903-1.51070.38972460.3714515896
1.5107-1.53230.34212730.3559514496
1.5323-1.55520.38512800.3459512396
1.5552-1.57950.33212510.3315516497
1.5795-1.60540.33442750.309517997
1.6054-1.63310.30252200.2856522797
1.6331-1.66270.32452510.2565513897
1.6627-1.69470.26032610.2481521397
1.6947-1.72930.27412790.2429519297
1.7293-1.76690.27312870.2279516497
1.7669-1.8080.26072560.214527398
1.808-1.85330.23442510.2043520297
1.8533-1.90340.23972680.2132527498
1.9034-1.95940.26842960.2083519598
1.9594-2.02260.22882920.1967520698
2.0226-2.09490.23282980.1958521098
2.0949-2.17880.22242460.1944529798
2.1788-2.2780.2562980.1915526198
2.278-2.39810.25852500.1938529999
2.3981-2.54830.22583030.1937529999
2.5483-2.74510.19032090.188537799
2.7451-3.02130.2462800.1957537099
3.0213-3.45840.2332730.1836534599
3.4584-4.3570.20822830.1747535899
4.357-55.9660.22692750.2064548699

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