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- PDB-6afg: DJ-1 with compound 9 -

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Basic information

Entry
Database: PDB / ID: 6afg
TitleDJ-1 with compound 9
ComponentsProtein/nucleic acid deglycase DJ-1
KeywordsHYDROLASE / DJ-1 / Parkinson's disease / Drug discovery / Fragment-based drug discovery
Function / homology
Function and homology information


tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / : / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate ...tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / : / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly / negative regulation of TRAIL-activated apoptotic signaling pathway / positive regulation of pyrroline-5-carboxylate reductase activity / positive regulation of tyrosine 3-monooxygenase activity / positive regulation of L-dopa biosynthetic process / positive regulation of L-dopa decarboxylase activity / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / glyoxalase (glycolic acid-forming) activity / negative regulation of protein K48-linked deubiquitination / negative regulation of ubiquitin-specific protease activity / protein deglycation, glyoxal removal / guanine deglycation, glyoxal removal / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / glyoxal metabolic process / guanine deglycation / positive regulation of NAD(P)H oxidase activity / glycolate biosynthetic process / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / protein deglycase activity / positive regulation of dopamine biosynthetic process / positive regulation of autophagy of mitochondrion / superoxide dismutase copper chaperone activity / positive regulation of acute inflammatory response to antigenic stimulus / oxidoreductase activity, acting on peroxide as acceptor / lactate biosynthetic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular detoxification of aldehyde / positive regulation of superoxide dismutase activity / small protein activating enzyme binding / Hydrolases; Acting on ester bonds; Thioester hydrolases / peroxiredoxin activity / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of ubiquitin-protein transferase activity / detoxification of copper ion / negative regulation of protein acetylation / positive regulation of transcription regulatory region DNA binding / positive regulation of androgen receptor activity / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / protein deglycosylation / membrane hyperpolarization / negative regulation of protein sumoylation / negative regulation of protein export from nucleus / regulation of androgen receptor signaling pathway / cupric ion binding / oxygen sensor activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / insulin secretion / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / positive regulation of reactive oxygen species biosynthetic process / nuclear androgen receptor binding / dopamine uptake involved in synaptic transmission / hydrogen peroxide metabolic process / ubiquitin-specific protease binding / cytokine binding / cuprous ion binding / membrane depolarization / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / single fertilization / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / negative regulation of protein ubiquitination / activation of protein kinase B activity / mitochondrion organization / adult locomotory behavior / SUMOylation of transcription cofactors / negative regulation of protein phosphorylation / regulation of mitochondrial membrane potential / negative regulation of protein binding / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / adherens junction / Late endosomal microautophagy / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / mitochondrial intermembrane space / PML body / autophagy / kinase binding
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-methylindole-2,3-dione / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCaaveiro, J.M.M. / Tashiro, S. / Tsumoto, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)Platform for Drug Discovery, Informatics and Structural Life Science Japan
Japan Society for the Promotion of Science25249115 Japan
Japan Society for the Promotion of Science16H02420 Japan
Japan Society for the Promotion of Science15K06962 Japan
Citation
Journal: ACS Chem. Biol. / Year: 2018
Title: Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
Authors: Tashiro, S. / Caaveiro, J.M.M. / Nakakido, M. / Tanabe, A. / Nagatoishi, S. / Tamura, Y. / Matsuda, N. / Liu, D. / Hoang, Q.Q. / Tsumoto, K.
#1: Journal: Biochemistry / Year: 2014
Title: Thermodynamic and structural characterization of the specific binding of Zn(II) to human protein DJ-1.
Authors: Tashiro, S. / Caaveiro, J.M.M. / Wu, C.X. / Hoang, Q.Q. / Tsumoto, K.
History
DepositionAug 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein/nucleic acid deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2393
Polymers19,9171
Non-polymers3222
Water4,035224
1
A: Protein/nucleic acid deglycase DJ-1
hetero molecules

A: Protein/nucleic acid deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4796
Polymers39,8342
Non-polymers6454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2840 Å2
ΔGint-20 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.450, 75.450, 75.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

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Components

#1: Protein Protein/nucleic acid deglycase DJ-1 / Maillard deglycase / Oncogene DJ1 / Parkinson disease protein 7 / Parkinsonism-associated deglycase ...Maillard deglycase / Oncogene DJ1 / Parkinson disease protein 7 / Parkinsonism-associated deglycase / Protein DJ-1 / DJ-1


Mass: 19917.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Plasmid: pET28B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q99497, Hydrolases; Acting on ester bonds; Thioester hydrolases, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, protein deglycase
#2: Chemical ChemComp-72V / 1-methylindole-2,3-dione


Mass: 161.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsThere are two reaction forms of 72V in this structure. 72V(201) is bonded with Cys106 through a ...There are two reaction forms of 72V in this structure. 72V(201) is bonded with Cys106 through a double bond opening, and 72V(202) is bonded to Lys148 through Schiff base.

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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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM TRIS-HCl, 200mM sodium citrate, 30% PEG 400, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→26.7 Å / Num. obs: 40321 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 7 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.746 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLM7.0.9data reduction
SCALA3.3.21data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SOA

1soa


Resolution: 1.5→26.7 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.032 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.048 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14795 2017 5 %RANDOM
Rwork0.11643 ---
obs0.11802 38272 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.851 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.5→26.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 23 224 1623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191502
X-RAY DIFFRACTIONr_bond_other_d0.0010.021533
X-RAY DIFFRACTIONr_angle_refined_deg1.5382.0232038
X-RAY DIFFRACTIONr_angle_other_deg0.8963.0043555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5085206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73125.6653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48915283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.528157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211696
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02289
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.182.135778
X-RAY DIFFRACTIONr_mcbond_other2.1752.131777
X-RAY DIFFRACTIONr_mcangle_it2.3523.203976
X-RAY DIFFRACTIONr_mcangle_other2.3563.206977
X-RAY DIFFRACTIONr_scbond_it3.3472.507724
X-RAY DIFFRACTIONr_scbond_other3.3462.508725
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4963.6031054
X-RAY DIFFRACTIONr_long_range_B_refined4.319.4481870
X-RAY DIFFRACTIONr_long_range_B_other3.64718.0781737
X-RAY DIFFRACTIONr_rigid_bond_restr3.06933035
X-RAY DIFFRACTIONr_sphericity_free30.264565
X-RAY DIFFRACTIONr_sphericity_bonded12.16453166
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 148 -
Rwork0.207 2829 -
obs--100 %

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