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- PDB-2rk3: Structure of A104T DJ-1 -

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Basic information

Entry
Database: PDB / ID: 2rk3
TitleStructure of A104T DJ-1
ComponentsProtein DJ-1
KeywordsCHAPERONE / PARKINSON'S DISEASE / THIJ / PFPI / Cytoplasm / Disease mutation / Nucleus / Oncogene / Oxidation / Parkinson disease / Phosphorylation / 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, methylglyoxal removal / : / 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 / : / 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 / guanine deglycation, glyoxal removal / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / glyoxal metabolic process / guanine deglycation / positive regulation of NAD(P)H oxidase activity / glycolate biosynthetic process / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / protein deglycase activity / 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 / oxidoreductase activity, acting on peroxide as acceptor / 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 / peroxiredoxin activity / 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 transcription regulatory region DNA binding / positive regulation of androgen receptor activity / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / protein deglycosylation / membrane hyperpolarization / negative regulation of protein sumoylation / negative regulation of protein export from nucleus / regulation of androgen receptor signaling pathway / cupric ion binding / oxygen sensor activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / insulin secretion / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / positive regulation of reactive oxygen species biosynthetic process / dopamine uptake involved in synaptic transmission / nuclear androgen receptor binding / hydrogen peroxide metabolic process / ubiquitin-specific protease binding / cytokine binding / cuprous ion binding / membrane depolarization / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / single fertilization / 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 / negative regulation of protein phosphorylation / regulation of mitochondrial membrane potential / negative regulation of protein binding / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / adherens junction / Late endosomal microautophagy / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / mitochondrial intermembrane space / PML body / autophagy / 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
Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsLakshminarasimhan, M. / Maldonado, M.T. / Zhou, W. / Fink, A.L. / Wilson, M.A.
CitationJournal: Biochemistry / Year: 2008
Title: Structural Impact of Three Parkinsonism-Associated Missense Mutations on Human DJ-1.
Authors: Lakshminarasimhan, M. / Maldonado, M.T. / Zhou, W. / Fink, A.L. / Wilson, M.A.
History
DepositionOct 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein DJ-1


Theoretical massNumber of molelcules
Total (without water)21,0181
Polymers21,0181
Non-polymers00
Water4,125229
1
A: Protein DJ-1

A: Protein DJ-1


Theoretical massNumber of molelcules
Total (without water)42,0362
Polymers42,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.780, 74.780, 74.990
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-359-

HOH

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Components

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


Mass: 21018.232 Da / Num. of mol.: 1 / Mutation: A104T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99497
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 3000, 100 mM HEPES, 200 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2005
RadiationMonochromator: Single Crystal Bent Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. all: 110339 / Num. obs: 110339 / % possible obs: 97.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 33.9
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.6 / Num. unique all: 10567 / % possible all: 94.5

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P5F

1p5f


Resolution: 1.05→50 Å / Num. parameters: 15298 / Num. restraintsaints: 19492 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1503 5523 5 %RANDOM
Rwork0.1321 ---
all0.1333 110293 --
obs0.1333 110293 97.8 %-
Solvent computationSolvent model: BABINET
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 1409 / Occupancy sum non hydrogen: 1604
Refinement stepCycle: LAST / Resolution: 1.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 0 229 1698
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0303
X-RAY DIFFRACTIONs_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.111
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.032
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0.11

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