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- PDB-4p2g: Crystal structure of DJ-1 in sulfinic acid form (aged crystal) -

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Basic information

Entry
Database: PDB / ID: 4p2g
TitleCrystal structure of DJ-1 in sulfinic acid form (aged crystal)
ComponentsProtein DJ-1
KeywordsHYDROLASE / Parkinson's disease / Sufinic acid Oxidation
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 / 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 / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / lactate biosynthetic process / positive regulation of acute inflammatory response to antigenic stimulus / protein repair / peptidase inhibitor activity / cellular detoxification of aldehyde / peroxiredoxin activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / small protein activating enzyme binding / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / detoxification of copper ion / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein sumoylation / 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 / membrane hyperpolarization / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / oxygen sensor activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / insulin secretion / ubiquitin-like protein conjugating enzyme binding / nuclear androgen receptor binding / hydrogen peroxide metabolic process / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / cytokine binding / positive regulation of reactive oxygen species biosynthetic process / cuprous ion binding / androgen receptor signaling pathway / regulation of neuron apoptotic process / signaling receptor activator activity / membrane depolarization / regulation of synaptic vesicle endocytosis / single fertilization / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / regulation of mitochondrial membrane potential / removal of superoxide radicals / SUMOylation of transcription cofactors / adult locomotory behavior / Late endosomal microautophagy / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / mitochondrion organization / adherens junction / positive regulation of protein-containing complex assembly / enzyme activator activity / PML body / Chaperone Mediated Autophagy / mitochondrial intermembrane space / autophagy / Aggrephagy / positive regulation of protein localization to nucleus / kinase binding / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / synaptic vesicle / glucose homeostasis / peptidase activity / cell body / cellular response to oxidative stress / regulation of inflammatory response / scaffold protein binding / DNA-binding transcription factor binding / response to oxidative stress
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
Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsTashiro, S. / Wu, C.-X. / Hoang, Q.Q. / Caaveiro, J.M.M. / Tsumoto, K.
CitationJournal: 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. / Wu, C.X. / Hoang, Q.Q. / Tsumoto, K.
History
DepositionMar 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Jul 23, 2014Group: Structure summary
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.4Nov 13, 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: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2493
Polymers19,9491
Non-polymers3002
Water4,828268
1
A: Protein DJ-1
hetero molecules

A: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4996
Polymers39,8982
Non-polymers6014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3870 Å2
ΔGint-12 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.760, 74.760, 75.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein DJ-1 / Oncogene DJ1 / Parkinson disease protein 7


Mass: 19949.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q99497, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 200 mM sodium citrate 30% (v:v) PEG400

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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 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→64.74 Å / Num. obs: 53628 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.2
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 7 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 5.5 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SOA

1soa


Resolution: 1.35→29.7 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.865 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12012 1525 2.8 %RANDOM
Rwork0.09789 ---
obs0.09852 52067 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.646 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.35→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1377 0 20 268 1665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191514
X-RAY DIFFRACTIONr_bond_other_d0.0010.021551
X-RAY DIFFRACTIONr_angle_refined_deg2.0732.0182051
X-RAY DIFFRACTIONr_angle_other_deg0.9043.0023578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34925.53656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18915288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.921158
X-RAY DIFFRACTIONr_chiral_restr0.1290.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
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_it2.3441.379785
X-RAY DIFFRACTIONr_mcbond_other2.0261.373784
X-RAY DIFFRACTIONr_mcangle_it1.942.066990
X-RAY DIFFRACTIONr_mcangle_other2.0882.07991
X-RAY DIFFRACTIONr_scbond_it3.4891.781729
X-RAY DIFFRACTIONr_scbond_other3.4791.779729
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4482.51053
X-RAY DIFFRACTIONr_long_range_B_refined3.99213.7691960
X-RAY DIFFRACTIONr_long_range_B_other3.23211.9941767
X-RAY DIFFRACTIONr_rigid_bond_restr5.14633065
X-RAY DIFFRACTIONr_sphericity_free24.372569
X-RAY DIFFRACTIONr_sphericity_bonded9.16753249
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.151 121 -
Rwork0.107 3806 -
obs--100 %

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