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- PDB-9cmy: Human DJ-1, 6.5-18.5 min mixing with methylglyoxal, fixed target ... -

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Basic information

Entry
Database: PDB / ID: 9cmy
TitleHuman DJ-1, 6.5-18.5 min mixing with methylglyoxal, fixed target serial crystallography
ComponentsProtein deglycase DJ-1
KeywordsHYDROLASE / Glutathione-independent glyoxalase / fixed target / microcrystals
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 / detoxification of mercury ion / ubiquitin-protein transferase inhibitor activity / methylglyoxal metabolic process / 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 / positive regulation of protein localization to nucleus / autophagy / kinase binding / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / Chaperone Mediated Autophagy / Aggrephagy / synaptic vesicle / glucose homeostasis / peptidase activity / cell body / regulation of inflammatory response / response to oxidative stress / cellular 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-like
Similarity search - Domain/homology
Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 Å
AuthorsZielinski, K. / Dolamore, C. / Dalton, K. / Meisburger, S. / Smith, N. / Termini, J. / Henning, R. / Srajer, V. / Hekstra, D. / Pollack, L. / Wilson, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM153337 United States
CitationJournal: Biorxiv / Year: 2024
Title: Resolving DJ-1 Glyoxalase Catalysis Using Mix-and-Inject Serial Crystallography at a Synchrotron.
Authors: Zielinski, K.A. / Dolamore, C. / Dalton, K.M. / Smith, N. / Termini, J. / Henning, R. / Srajer, V. / Hekstra, D.R. / Pollack, L. / Wilson, M.A.
History
DepositionJul 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein deglycase DJ-1


Theoretical massNumber of molelcules
Total (without water)20,1991
Polymers20,1991
Non-polymers00
Water1,65792
1
A: Protein deglycase DJ-1

A: Protein deglycase DJ-1


Theoretical massNumber of molelcules
Total (without water)40,3992
Polymers40,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2720 Å2
ΔGint-15 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.234, 76.234, 76.392
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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


Mass: 20199.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q99497, Hydrolases; Acting on ester bonds; Thioester hydrolases, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.17 Å3/Da / Density % sol: 61.23 % / Description: 20-25 micron microcrystals
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5 / Details: 100 mM HEPES, 200 mM NaCl, 15% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.969 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.69→66.02 Å / Num. obs: 28986 / % possible obs: 99.31 % / Redundancy: 12.8 % / Biso Wilson estimate: 25.75 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.295 / Net I/σ(I): 6.6
Reflection shellResolution: 1.69→1.72 Å / Rmerge(I) obs: 5.56 / Num. unique obs: 1428 / CC1/2: 0.066 / % possible all: 99.86
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Microcrystals raster scanned on a grid

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
DIALSdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.69→49.95 Å / SU ML: 0.1729 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.4853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1751 1931 6.68 %
Rwork0.1572 26978 -
obs0.1584 28909 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.57 Å2
Refinement stepCycle: LAST / Resolution: 1.69→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1383 0 0 92 1475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741505
X-RAY DIFFRACTIONf_angle_d0.77862049
X-RAY DIFFRACTIONf_chiral_restr0.0546239
X-RAY DIFFRACTIONf_plane_restr0.0073274
X-RAY DIFFRACTIONf_dihedral_angle_d13.4955586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.33341550.29571855X-RAY DIFFRACTION97.91
1.73-1.780.30311130.2841921X-RAY DIFFRACTION98.79
1.78-1.830.30171270.27621910X-RAY DIFFRACTION99.27
1.83-1.890.26491440.22941900X-RAY DIFFRACTION99.56
1.89-1.960.24781250.20591950X-RAY DIFFRACTION99.57
1.96-2.040.2031530.17881896X-RAY DIFFRACTION99.56
2.04-2.130.15651270.17241928X-RAY DIFFRACTION99.47
2.13-2.240.17891300.16111939X-RAY DIFFRACTION99.66
2.24-2.380.17161420.15341913X-RAY DIFFRACTION99.52
2.38-2.570.16211530.14481916X-RAY DIFFRACTION99.47
2.57-2.820.1581310.15041942X-RAY DIFFRACTION99.09
2.82-3.230.19221350.14951937X-RAY DIFFRACTION98.95
3.23-4.070.15991580.1311937X-RAY DIFFRACTION98.4
4.07-49.950.13411380.13392034X-RAY DIFFRACTION97.62

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