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- PDB-5dak: Crystal Structure of human Glutathione Transferase Pi complexed w... -

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Basic information

Entry
Database: PDB / ID: 5dak
TitleCrystal Structure of human Glutathione Transferase Pi complexed with a metalloid in the absence of Glutathione
Components(Glutathione S-transferase P) x 2
KeywordsTRANSFERASE / Metalloid / Anti-cancer
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 / negative regulation of interleukin-1 beta production / cellular response to glucocorticoid stimulus / 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
ARSENIC / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsParker, L.J. / Parker, M.W. / Morton, C.J.
CitationJournal: To Be Published
Title: Visualisation of Organoarsenic Human Glutathione Transferase P1-1 Complexes: Metabolism of Arsenic-based Therapeutics
Authors: Parker, L.J. / Parker, M.W. / Morton, C.J. / Bocedi, A. / Ascher, D.B. / Aitken, J.B. / Harris, H.H. / Lo Bello, M. / Ricci, G.
History
DepositionAug 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,3126
Polymers46,7722
Non-polymers5404
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-16 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.629, 95.509, 68.247
Angle α, β, γ (deg.)90.000, 98.260, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

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Components

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


Mass: 23377.770 Da / Num. of mol.: 1
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
#2: Protein Glutathione S-transferase P / GST class-pi / GSTP1-1


Mass: 23393.770 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: As
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100MM MES, PH 6.0, 28% (W/V) PEG 8000, 20MM CACL2 10MM DTT. Soaked in 2mM PAO dissolved in DMSO
PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.11→47.75 Å / Num. obs: 50403 / % possible obs: 94.5 % / Redundancy: 11.6 % / Biso Wilson estimate: 22.43 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.039 / Net I/σ(I): 11 / Num. measured all: 297531 / Scaling rejects: 432
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.11-2.184.70.4972.534997500.6790.22433.5
8.97-47.75110.06619.941453780.9980.0299.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
Aimless0.5.4data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5GSS

5gss


Resolution: 2.11→46.902 Å / FOM work R set: 0.8514 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.51 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 2559 5.08 %Random Selection
Rwork0.157 47844 --
obs0.1594 50403 94.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.21 Å2 / Biso mean: 25.7 Å2 / Biso min: 7.78 Å2
Refinement stepCycle: final / Resolution: 2.11→46.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 58 239 3313
Biso mean--41.75 30.55 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123111
X-RAY DIFFRACTIONf_angle_d1.4214224
X-RAY DIFFRACTIONf_chiral_restr0.074472
X-RAY DIFFRACTIONf_plane_restr0.007546
X-RAY DIFFRACTIONf_dihedral_angle_d14.6481160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.15490.3553180.346329531311
2.1549-2.19890.28261330.2152524265789
2.1989-2.24670.22441550.178828292984100
2.2467-2.2990.24081680.166827832951100
2.299-2.35650.23251630.160928102973100
2.3565-2.42020.21221460.15828132959100
2.4202-2.49140.27381410.162428362977100
2.4914-2.57180.20871540.153428102964100
2.5718-2.66370.26041440.15728112955100
2.6637-2.77040.22441770.160227722949100
2.7704-2.89650.23931440.169428482992100
2.8965-3.04910.20821330.166327832916100
3.0491-3.24010.22141570.163328242981100
3.2401-3.49020.18081470.151128132960100
3.4902-3.84130.18111300.146628362966100
3.8413-4.39680.16471500.131928192969100
4.3968-5.53810.15781570.13528292986100
5.5381-46.91340.19321420.17528092951100

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