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

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Basic information

Entry
Database: PDB / ID: 4mnt
TitleCrystal structure of human DJ-1 in complex with Cu
ComponentsProtein DJ-1
KeywordsHYDROLASE / protein-metal complex / Flavodoxin-like fold / Rossmann fold / chaperone / Copper binding / Cysteine Oxidation
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, glyoxal removal / protein deglycation, methylglyoxal removal / : / detoxification of hydrogen peroxide ...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, glyoxal removal / protein deglycation, methylglyoxal removal / : / 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 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 ubiquitin-specific protease activity / negative regulation of protein K48-linked deubiquitination / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / positive regulation of NAD(P)H oxidase activity / glycolate biosynthetic process / detection of oxidative stress / glyoxal metabolic process / guanine deglycation / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / protein deglycase activity / oxidoreductase activity, acting on peroxide as acceptor / 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 / positive regulation of superoxide dismutase activity / lactate biosynthetic process / : / cellular detoxification of aldehyde / protein deglycosylation / positive regulation of transcription regulatory region DNA binding / small protein activating enzyme binding / peroxiredoxin activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / 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 oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of androgen receptor activity / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of protein sumoylation / membrane hyperpolarization / negative regulation of protein export from nucleus / regulation of androgen receptor signaling pathway / cupric ion binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / insulin secretion / ubiquitin-like protein conjugating enzyme binding / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / oxygen sensor activity / 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 / cuprous ion binding / cytokine binding / membrane depolarization / single fertilization / 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 / activation of protein kinase B activity / adult locomotory behavior / SUMOylation of transcription cofactors / negative regulation of protein phosphorylation / negative regulation of protein binding / regulation of mitochondrial membrane potential / positive regulation of interleukin-8 production / mitochondrion organization / negative regulation of extrinsic apoptotic signaling pathway / adherens junction / positive regulation of DNA-binding transcription factor activity / negative regulation of protein kinase activity / Late endosomal microautophagy / positive regulation of protein-containing complex assembly / PML body / mitochondrial intermembrane space / 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
COPPER (II) ION / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.584 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
DepositionSep 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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)20,0443
Polymers19,9171
Non-polymers1272
Water5,044280
1
A: Protein DJ-1
hetero molecules

A: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0886
Polymers39,8342
Non-polymers2544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3150 Å2
ΔGint-60 kcal/mol
Surface area14720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.240, 75.240, 75.300
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-202-

CU

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Components

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


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: 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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Sodium Malonate, 20% w/v PEG 3350, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.378 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2010
RadiationMonochromator: vertically collimating mirror (focus at infinity), followed by a Bartels Monochromator with dual channel cut crystals (DCCM) and a toroidal mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.378 Å / Relative weight: 1
ReflectionResolution: 1.58→24.64 Å / Num. all: 33930 / Num. obs: 33930 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.5 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 7.5
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameClassification
iMOSFLMdata reduction
PHASERphasing
PHENIXrefinement
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.584→24.628 Å / SU ML: 0.14 / σ(F): 1.38 / Phase error: 15.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1774 1717 5.07 %
Rwork0.1508 --
obs0.1521 33891 99.95 %
all-33940 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.584→24.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 2 280 1656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061397
X-RAY DIFFRACTIONf_angle_d1.1171889
X-RAY DIFFRACTIONf_dihedral_angle_d12.235529
X-RAY DIFFRACTIONf_chiral_restr0.073225
X-RAY DIFFRACTIONf_plane_restr0.005246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.584-1.60770.23421380.19122647X-RAY DIFFRACTION100
1.6077-1.63280.2241240.17542729X-RAY DIFFRACTION100
1.6328-1.65960.18531420.16952614X-RAY DIFFRACTION100
1.6596-1.68820.1821370.16822702X-RAY DIFFRACTION100
1.6882-1.71890.18121600.16462669X-RAY DIFFRACTION100
1.7189-1.75190.1981340.16462691X-RAY DIFFRACTION100
1.7519-1.78770.23381750.16082602X-RAY DIFFRACTION100
1.7877-1.82650.13391360.16052705X-RAY DIFFRACTION100
1.8265-1.8690.17131720.15292669X-RAY DIFFRACTION100
1.869-1.91570.19721270.15832665X-RAY DIFFRACTION100
1.9157-1.96750.1751600.14592656X-RAY DIFFRACTION100
1.9675-2.02540.18771420.15332691X-RAY DIFFRACTION100
2.0254-2.09070.15291480.15162709X-RAY DIFFRACTION100
2.0907-2.16540.21411370.14912633X-RAY DIFFRACTION100
2.1654-2.2520.17911490.15262669X-RAY DIFFRACTION100
2.252-2.35440.19451410.15712687X-RAY DIFFRACTION100
2.3544-2.47850.19461410.15242664X-RAY DIFFRACTION100
2.4785-2.63360.21751490.16432695X-RAY DIFFRACTION100
2.6336-2.83660.17411630.15582642X-RAY DIFFRACTION100
2.8366-3.12160.14851300.15512692X-RAY DIFFRACTION100
3.1216-3.57210.1641210.14082712X-RAY DIFFRACTION100
3.5721-4.4960.1411350.12652661X-RAY DIFFRACTION100
4.496-24.6310.17741220.14432704X-RAY DIFFRACTION100

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