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- PDB-3b38: Structure of A104V DJ-1 -

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Basic information

Entry
Database: PDB / ID: 3b38
TitleStructure of A104V DJ-1
ComponentsProtein DJ-1
KeywordsCHAPERONE / PARKINSON'S DISEASE / PFPI / THIJ / Cytoplasm / Disease mutation / Nucleus / Oncogene / Oxidation / Parkinson disease / Phosphorylation / Polymorphism / Ubl conjugation
Function / homology
Function and homology information


positive regulation of acute inflammatory response to antigenic stimulus / 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 ...positive regulation of acute inflammatory response to antigenic stimulus / 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 / hydrogen peroxide metabolic process / positive regulation of dopamine biosynthetic process / protein deglycase activity / positive regulation of autophagy of mitochondrion / superoxide dismutase copper chaperone activity / oxidoreductase activity, acting on peroxide as acceptor / positive regulation of mitochondrial electron transport, NADH to ubiquinone / lactate biosynthetic process / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / 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 / negative regulation of protein sumoylation / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein export from nucleus / cupric ion binding / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of androgen receptor signaling pathway / membrane hyperpolarization / oxygen sensor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / insulin secretion / ubiquitin-like protein conjugating enzyme binding / nuclear androgen receptor binding / androgen receptor signaling pathway / ubiquitin-specific protease binding / cytokine binding / dopamine uptake involved in synaptic transmission / positive regulation of reactive oxygen species biosynthetic process / cuprous ion binding / 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 / 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 / removal of superoxide radicals / SUMOylation of transcription cofactors / adult locomotory behavior / regulation of mitochondrial membrane potential / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / mitochondrion organization / adherens junction / positive regulation of protein-containing complex assembly / enzyme activator activity / Late endosomal microautophagy / PML body / mitochondrial intermembrane space / autophagy / positive regulation of protein localization to nucleus / kinase binding / cellular response to hydrogen peroxide / Chaperone Mediated Autophagy / positive regulation of reactive oxygen species metabolic process / Aggrephagy / synaptic vesicle / glucose homeostasis / peptidase activity / cell body / regulation of inflammatory response / cellular response to oxidative stress / response to oxidative stress / scaffold protein binding / DNA-binding transcription factor 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 / MOLECULAR REPLACEMENT / Resolution: 1.85 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 19, 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 / Derived calculations / Category: 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6628
Polymers20,2271
Non-polymers4347
Water3,405189
1
A: Protein DJ-1
hetero molecules

A: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,32416
Polymers40,4552
Non-polymers86914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area4990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.842, 66.842, 175.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 20227.381 Da / Num. of mol.: 1 / Mutation: A104V
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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 10, 2007
RadiationMonochromator: OSMIC BLUE CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.85→57.93 Å / Num. all: 20778 / Num. obs: 20778 / % possible obs: 99.8 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 31.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2025 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P5F

1p5f


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.231 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.121 / ESU R Free: 0.123 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1064 5.1 %RANDOM
Rwork0.18133 ---
all0.18346 19656 --
obs0.18346 19656 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1420 0 28 189 1637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221461
X-RAY DIFFRACTIONr_angle_refined_deg1.3392.0011962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36525.29451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94715262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.326157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021056
X-RAY DIFFRACTIONr_nbd_refined0.2020.2729
X-RAY DIFFRACTIONr_nbtor_refined0.30.2977
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.214
X-RAY DIFFRACTIONr_mcbond_it0.7911.5997
X-RAY DIFFRACTIONr_mcangle_it1.21821533
X-RAY DIFFRACTIONr_scbond_it2.093521
X-RAY DIFFRACTIONr_scangle_it3.3514.5429
LS refinement shellResolution: 1.85→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 96 -
Rwork0.28 1369 -
obs--98.99 %

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