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

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Basic information

Entry
Database: PDB / ID: 5dal
TitleCrystal Structure of human Glutathione Transferase Pi complexed with a metalloid in the presence of Glutathione
Components(Glutathione S-transferase ...) 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
Di-glutathione-PhenylArsine / GLUTATHIONE / Phenylarsine oxide / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,73811
Polymers46,7722
Non-polymers2,9679
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-34 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.550, 90.220, 68.670
Angle α, β, γ (deg.)90.000, 98.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-582-

HOH

21B-613-

HOH

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Components

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Glutathione S-transferase ... , 2 types, 2 molecules AB

#1: 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
#2: 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

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Non-polymers , 6 types, 489 molecules

#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-5AU / Di-glutathione-PhenylArsine


Mass: 764.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H37AsN6O12S2
#5: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#6: Chemical ChemComp-PA0 / Phenylarsine oxide / oxo(phenyl)arsane


Mass: 168.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5AsO
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100MM MES, PH 6.0, 28% (W/V) PEG 8000, 20MM CACL2, 10MM DTT, 10MM GSH. Soaked in 2MM PAO dissolved in DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→35.63 Å / Num. obs: 74367 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.99 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.032 / Net I/σ(I): 15.2 / Num. measured all: 508961 / Scaling rejects: 5242
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
1.5-1.5370.78722610137100.6380.31799.4
8.22-35.634.90.03956.717423580.9730.02173.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.5 Å35.63 Å
Translation1.5 Å35.63 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
Aimless0.5.8data scaling
PHASER2.5.3phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5GSS

5gss


Resolution: 1.5→34 Å / FOM work R set: 0.8681 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 3673 4.94 %Random Selection
Rwork0.1797 70686 --
obs0.1813 74359 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.15 Å2 / Biso mean: 21.36 Å2 / Biso min: 6.77 Å2
Refinement stepCycle: final / Resolution: 1.5→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 313 480 4070
Biso mean--28.12 29.6 -
Num. residues----419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113535
X-RAY DIFFRACTIONf_angle_d1.3964792
X-RAY DIFFRACTIONf_chiral_restr0.112521
X-RAY DIFFRACTIONf_plane_restr0.007622
X-RAY DIFFRACTIONf_dihedral_angle_d20.0741375
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51970.29381420.27822719286199
1.5197-1.54060.31921370.26412647278499
1.5406-1.56260.26191350.25072768290399
1.5626-1.58590.25931270.22962683281099
1.5859-1.61070.25771470.230427512898100
1.6107-1.63710.24751230.22627252848100
1.6371-1.66530.25181320.211227182850100
1.6653-1.69560.26071660.203526912857100
1.6956-1.72820.22941390.199827112850100
1.7282-1.76350.21941320.192427282860100
1.7635-1.80180.2531530.197527242877100
1.8018-1.84370.25441390.186626862825100
1.8437-1.88980.20011690.189126942863100
1.8898-1.94090.20581410.177326942835100
1.9409-1.9980.21041370.172527272864100
1.998-2.06250.22621370.180227802917100
2.0625-2.13620.18461320.174827142846100
2.1362-2.22170.18971410.161227292870100
2.2217-2.32280.21051560.156926952851100
2.3228-2.44530.21261310.156927592890100
2.4453-2.59840.19921430.150227312874100
2.5984-2.79890.19911440.162227352879100
2.7989-3.08040.21951370.174327532890100
3.0804-3.52580.20521550.169527422897100
3.5258-4.44060.1961470.155227222869100
4.4406-34.00870.18421310.20432660279194

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