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- PDB-3bwe: Crystal structure of aggregated form of DJ1 -

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Basic information

Entry
Database: PDB / ID: 3bwe
TitleCrystal structure of aggregated form of DJ1
ComponentsProtein DJ-1
KeywordsCHAPERONE / DJ-1 / filamentous aggregates / Cytoplasm / Disease mutation / Nucleus / Oncogene / Oxidation / Parkinson disease / Phosphoprotein / Polymorphism / Ubl conjugation
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
PHOSPHATE ION / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCha, S.S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of filamentous aggregates of human DJ-1 formed in an inorganic phosphate-dependent manner.
Authors: Cha, S.S. / Jung, H.I. / Jeon, H. / An, Y.J. / Kim, I.K. / Yun, S. / Ahn, H.J. / Chung, K.C. / Lee, S.H. / Suh, P.G. / Kang, S.O.
History
DepositionJan 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 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
B: Protein DJ-1
C: Protein DJ-1
D: Protein DJ-1
E: Protein DJ-1
F: Protein DJ-1
G: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,72514
Polymers141,0617
Non-polymers6657
Water5,098283
1
A: Protein DJ-1
B: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4934
Polymers40,3032
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-32 kcal/mol
Surface area14650 Å2
MethodPISA
2
C: Protein DJ-1
D: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4934
Polymers40,3032
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-33.4 kcal/mol
Surface area14690 Å2
MethodPISA
3
E: Protein DJ-1
F: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5885
Polymers40,3032
Non-polymers2853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-33.5 kcal/mol
Surface area14240 Å2
MethodPISA
4
G: Protein DJ-1

G: Protein DJ-1


Theoretical massNumber of molelcules
Total (without water)40,3032
Polymers40,3032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3090 Å2
ΔGint-34.9 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.616, 102.582, 85.535
Angle α, β, γ (deg.)90.00, 113.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 20151.525 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99497
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growMethod: evaporation / Details: EVAPORATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.12714 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 56724 / % possible obs: 98.62 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.4→2.4 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J42

1j42


Resolution: 2.4→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 58196.92 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 5760 10.2 %random
Rwork0.232 ---
obs0.232 56652 94.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.78 Å21.71 Å22.06 Å2
2--0 Å23.36 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9490 0 35 283 9808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.7
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 951 10.2 %
Rwork0.33 8338 -
obs--93.3 %

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