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- PDB-4n0m: Crystal structure of human C53A DJ-1 in complex with Cu -

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Basic information

Entry
Database: PDB / ID: 4n0m
TitleCrystal structure of human C53A DJ-1 in complex with Cu
ComponentsProtein DJ-1
KeywordsHYDROLASE / homodimer / copper binding / Rossmann fold / alpha/beta protein / chaperone / oxidative stress protection / cytosol / mitochondrion / nucleus
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 / glutathione deglycation / 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 / glutathione deglycation / 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 / glycolate biosynthetic process / guanine deglycation, glyoxal removal / glyoxal metabolic process / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / guanine deglycation / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / oxidoreductase activity, acting on peroxide as acceptor / protein deglycase activity / positive regulation of acute inflammatory response to antigenic stimulus / positive regulation of dopamine biosynthetic process / superoxide dismutase copper chaperone activity / positive regulation of NAD(P)H oxidase activity / positive regulation of autophagy of mitochondrion / 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 / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of ubiquitin-protein transferase activity / peroxiredoxin activity / detoxification of copper ion / negative regulation of protein acetylation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of transcription regulatory region DNA binding / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of androgen receptor activity / membrane hyperpolarization / protein deglycosylation / negative regulation of protein sumoylation / oxygen sensor activity / regulation of androgen receptor signaling pathway / negative regulation of protein export from nucleus / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / cupric ion binding / ubiquitin-like protein conjugating enzyme binding / insulin secretion / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / dopamine uptake involved in synaptic transmission / positive regulation of reactive oxygen species biosynthetic process / nuclear androgen receptor binding / hydrogen peroxide metabolic process / ubiquitin-specific protease binding / cytokine binding / cuprous ion binding / single fertilization / membrane depolarization / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / negative regulation of protein binding / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein-containing complex assembly / adherens junction / Late endosomal microautophagy / negative regulation of protein kinase activity / mitochondrial intermembrane space / PML body / cellular response to hydrogen peroxide / autophagy
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
COPPER (II) ION / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCendron, L. / Girotto, S. / Bisaglia, M. / Tessari, I. / Mammi, S. / Zanotti, G. / Bubacco, L.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: DJ-1 Is a Copper Chaperone Acting on SOD1 Activation.
Authors: Girotto, S. / Cendron, L. / Bisaglia, M. / Tessari, I. / Mammi, S. / Zanotti, G. / Bubacco, L.
History
DepositionOct 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0113
Polymers19,8851
Non-polymers1262
Water3,243180
1
A: Protein DJ-1
hetero molecules

A: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0216
Polymers39,7702
Non-polymers2514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area3380 Å2
ΔGint-36 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.140, 75.140, 75.271
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: 19884.986 Da / Num. of mol.: 1 / Mutation: C53A
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(DE3)
References: UniProt: Q99497, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.08 Å3/Da / Density % sol: 60.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Sodium Malonate, 20% w/v PEG 3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.378 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2011
RadiationMonochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.378 Å / Relative weight: 1
ReflectionResolution: 1.95→37.63 Å / Num. all: 18268 / Num. obs: 18268 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.114
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.351 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(autoMR)model building
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX(autoMR)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→32.58 Å / SU ML: 0.16 / σ(F): 1.39 / Phase error: 14.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.175 932 5.11 %
Rwork0.149 --
obs0.15 18238 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0964 Å20 Å20 Å2
2--0.0964 Å2-0 Å2
3----0.1928 Å2
Refinement stepCycle: LAST / Resolution: 1.95→32.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1373 0 5 180 1558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071414
X-RAY DIFFRACTIONf_angle_d1.2221911
X-RAY DIFFRACTIONf_dihedral_angle_d11.976536
X-RAY DIFFRACTIONf_chiral_restr0.076226
X-RAY DIFFRACTIONf_plane_restr0.005250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.05280.19441450.15662427X-RAY DIFFRACTION100
2.0528-2.18140.16021330.14212427X-RAY DIFFRACTION100
2.1814-2.34980.1911390.14122472X-RAY DIFFRACTION100
2.3498-2.58620.19581370.15282458X-RAY DIFFRACTION100
2.5862-2.96020.19181210.15722475X-RAY DIFFRACTION100
2.9602-3.72860.16031390.14962493X-RAY DIFFRACTION100
3.7286-32.58350.15991180.14482554X-RAY DIFFRACTION97

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