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- PDB-9cgd: Human DJ-1, 10 sec mixing with methylglyoxal, pink beam time-reso... -

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Basic information

Entry
Database: PDB / ID: 9cgd
TitleHuman DJ-1, 10 sec mixing with methylglyoxal, pink beam time-resolved serial crystallography, CrystFEL processed
ComponentsParkinson disease protein 7
KeywordsHYDROLASE / Glutathione-independent glyoxalase / mix-and-inject serial crystallography / Laue diffraction
Function / homology
Function and homology information


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 ...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 / protein deglycase activity / positive regulation of dopamine biosynthetic process / oxidoreductase activity, acting on peroxide as acceptor / positive regulation of autophagy of mitochondrion / superoxide dismutase copper chaperone activity / positive regulation of mitochondrial electron transport, NADH to ubiquinone / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / lactate biosynthetic process / positive regulation of acute inflammatory response to antigenic stimulus / protein repair / peptidase inhibitor activity / cellular detoxification of aldehyde / peroxiredoxin activity / small protein activating enzyme binding / Hydrolases; Acting on ester bonds; Thioester hydrolases / negative regulation of protein acetylation / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / detoxification of copper ion / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein sumoylation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of protein export from nucleus / membrane hyperpolarization / cupric ion binding / regulation of androgen receptor signaling pathway / insulin secretion / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / oxygen sensor activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / nuclear androgen receptor binding / hydrogen peroxide metabolic process / positive regulation of reactive oxygen species biosynthetic process / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / cytokine binding / signaling receptor activator activity / regulation of synaptic vesicle endocytosis / cuprous ion binding / androgen receptor signaling pathway / negative regulation of protein phosphorylation / 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 / removal of superoxide radicals / SUMOylation of transcription cofactors / positive regulation of peptidyl-serine phosphorylation / enzyme activator activity / regulation of mitochondrial membrane potential / adult locomotory behavior / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / adherens junction / mitochondrion organization / positive regulation of protein-containing complex assembly / Late endosomal microautophagy / PML body / mitochondrial intermembrane space / positive regulation of protein localization to nucleus / autophagy / kinase binding / cellular response to hydrogen peroxide / Chaperone Mediated Autophagy / Aggrephagy / positive regulation of reactive oxygen species metabolic process / synaptic vesicle / glucose homeostasis / peptidase activity / cell body / cellular response to oxidative stress / regulation of inflammatory response
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: 1.97 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
DepositionJun 28, 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: Parkinson disease protein 7


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water2,234124
1
A: Parkinson disease protein 7

A: Parkinson disease protein 7


Theoretical massNumber of molelcules
Total (without water)40,5432
Polymers40,5432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2830 Å2
ΔGint-17 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.030, 76.030, 76.140
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 Parkinson disease protein 7 / Maillard deglycase / Oncogene DJ1 / Parkinsonism-associated deglycase / Protein DJ-1 / DJ-1 / ...Maillard deglycase / Oncogene DJ1 / Parkinsonism-associated deglycase / Protein DJ-1 / DJ-1 / Protein/nucleic acid deglycase DJ-1


Mass: 20271.391 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, protein deglycase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.15 Å3/Da / Density % sol: 60.89 % / 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: APS / Beamline: 14-ID-B / Wavelength: 1.240-1.016
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Nov 13, 2022
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.241
21.0161
ReflectionResolution: 1.77→65.84 Å / Num. obs: 24998 / % possible obs: 99.01 % / Redundancy: 95.32 % / Biso Wilson estimate: 27.55 Å2 / CC1/2: 0.99 / R split: 0.101 / Net I/σ(I): 4.68
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 90.5 % / Mean I/σ(I) obs: 0.31 / Num. unique obs: 2428 / CC1/2: 0.05 / % possible all: 98.7
Serial crystallography sample deliveryDescription: concentric flow microfluidic mixer / Method: injection
Serial crystallography data reductionCrystal hits: 1518 / Frames indexed: 1477 / Frames total: 20000

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Precognitiondata reduction
CrystFELdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.97→32.96 Å / SU ML: 0.1935 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9654
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1772 902 4.95 %
Rwork0.1485 17334 -
obs0.15 18236 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.46 Å2
Refinement stepCycle: LAST / Resolution: 1.97→32.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1383 0 5 124 1512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591466
X-RAY DIFFRACTIONf_angle_d0.74151986
X-RAY DIFFRACTIONf_chiral_restr0.0488234
X-RAY DIFFRACTIONf_plane_restr0.006261
X-RAY DIFFRACTIONf_dihedral_angle_d13.4792567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.090.28411470.26562837X-RAY DIFFRACTION98.97
2.09-2.250.28651420.21082853X-RAY DIFFRACTION99.21
2.26-2.480.20761660.17882832X-RAY DIFFRACTION99.17
2.48-2.840.1721460.15422890X-RAY DIFFRACTION99.02
2.84-3.580.18431370.13752912X-RAY DIFFRACTION99.09
3.58-32.960.12851640.1093010X-RAY DIFFRACTION98.94

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