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- PDB-6afa: DJ-1 with isatin (low concentration) -

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Basic information

Entry
Database: PDB / ID: 6afa
TitleDJ-1 with isatin (low concentration)
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 / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / guanine deglycation, glyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly ...tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / guanine deglycation, glyoxal 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 L-dopa biosynthetic process / glyoxalase (glycolic acid-forming) activity / negative regulation of protein K48-linked deubiquitination / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / glycolate biosynthetic process / detection of oxidative stress / glyoxal metabolic process / guanine deglycation / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / methylglyoxal metabolic process / detoxification of mercury ion / ubiquitin-protein transferase inhibitor activity / protein deglycase / mercury ion binding / protein deglycase activity / positive regulation of dopamine biosynthetic process / oxidoreductase activity, acting on peroxide as acceptor / positive regulation of autophagy of mitochondrion / superoxide dismutase copper chaperone activity / positive regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of acute inflammatory response to antigenic stimulus / lactate biosynthetic process / protein repair / peptidase inhibitor activity / cellular detoxification of aldehyde / peroxiredoxin activity / small protein activating enzyme binding / Hydrolases; Acting on ester bonds; Thioester hydrolases / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / detoxification of copper ion / negative regulation of protein acetylation / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein sumoylation / membrane hyperpolarization / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of protein export from nucleus / cupric ion binding / regulation of androgen receptor signaling pathway / insulin secretion / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / oxygen sensor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / hydrogen peroxide metabolic process / nuclear androgen receptor binding / positive regulation of reactive oxygen species biosynthetic process / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / signaling receptor activator activity / cytokine binding / regulation of synaptic vesicle endocytosis / cuprous ion binding / androgen receptor signaling pathway / membrane depolarization / single fertilization / negative regulation of protein phosphorylation / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / enzyme activator activity / removal of superoxide radicals / SUMOylation of transcription cofactors / regulation of mitochondrial membrane potential / adult locomotory behavior / mitochondrion organization / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / adherens junction / positive regulation of protein-containing complex assembly / Late endosomal microautophagy / positive regulation of peptidyl-serine phosphorylation / PML body / mitochondrial intermembrane space / kinase binding / autophagy / cellular response to hydrogen peroxide / positive regulation of protein localization to nucleus / Chaperone Mediated Autophagy / Aggrephagy / positive regulation of reactive oxygen species metabolic process / glucose homeostasis / synaptic vesicle / peptidase activity / cell body / cellular response to oxidative stress / regulation of inflammatory response
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
ISATIN / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)20,1003
Polymers19,9171
Non-polymers1832
Water2,450136
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)40,1996
Polymers39,8342
Non-polymers3654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3820 Å2
ΔGint-23 kcal/mol
Surface area14720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.270, 75.270, 75.561
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-426-

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-ISN / ISATIN


Mass: 147.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5NO2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsISN201 is bonded with Cys106 through a double bond opening.

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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: 3.1 Å3/Da / Density % sol: 60.35 %
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: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→33.7 Å / Num. obs: 30043 / % possible obs: 99.6 % / Redundancy: 3.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.5
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.607 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLM7.1.0data reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SOA

1soa


Resolution: 1.65→33.7 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.527 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18693 1229 4.1 %RANDOM
Rwork0.14037 ---
obs0.1422 28810 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.773 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.65→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 12 136 1524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191422
X-RAY DIFFRACTIONr_bond_other_d0.0010.021433
X-RAY DIFFRACTIONr_angle_refined_deg1.4932.0011923
X-RAY DIFFRACTIONr_angle_other_deg0.823.0013309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9335190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69525.4951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52915256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.078157
X-RAY DIFFRACTIONr_chiral_restr0.0820.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211604
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02276
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_it2.6882.157754
X-RAY DIFFRACTIONr_mcbond_other2.6672.153753
X-RAY DIFFRACTIONr_mcangle_it2.9793.234943
X-RAY DIFFRACTIONr_mcangle_other2.9773.236944
X-RAY DIFFRACTIONr_scbond_it3.392.604668
X-RAY DIFFRACTIONr_scbond_other3.3872.605669
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1063.713980
X-RAY DIFFRACTIONr_long_range_B_refined4.35418.5131678
X-RAY DIFFRACTIONr_long_range_B_other4.13117.9811617
X-RAY DIFFRACTIONr_rigid_bond_restr3.12932854
X-RAY DIFFRACTIONr_sphericity_free24.153550
X-RAY DIFFRACTIONr_sphericity_bonded12.22252921
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 74 -
Rwork0.255 2147 -
obs--99.95 %

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