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- PDB-9yzv: Joint Xray/Neutron structure of human DJ-1 at room temperature -

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Basic information

Entry
Database: PDB / ID: 9yzv
TitleJoint Xray/Neutron structure of human DJ-1 at room temperature
ComponentsProtein deglycase DJ-1
KeywordsHYDROLASE / PARK7 / glyoxalase / cyclic phosphoglycerate anhydride hydrolase
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 / 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 / oxygen sensor activity / ubiquitin-like protein conjugating enzyme binding / insulin secretion / nuclear androgen receptor binding / androgen receptor signaling pathway / ubiquitin-specific protease binding / cytokine binding / positive regulation of reactive oxygen species biosynthetic process / dopamine uptake involved in synaptic transmission / 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 / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / regulation of mitochondrial membrane potential / mitochondrion organization / adherens junction / enzyme activator activity / 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 / 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 / NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsLin, J. / Kovalevsky, A. / Walker, A.R. / 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
Citation
Journal: To Be Published
Title: Environmental contributions to proton sharing in protein low barrier hydrogen bonds
Authors: Lin, J. / Gerlits, O. / Kneller, D.W. / Weiss, K.L. / Coates, L. / Hix, M.A. / Effah, S.Y. / Kovalevsky, A. / Walker, A.R. / Wilson, M.A.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2012
Polymers20,1991
Non-polymers21
Water2,324129
1
A: Protein deglycase DJ-1
hetero molecules

A: Protein deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4034
Polymers40,3992
Non-polymers42
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area3070 Å2
ΔGint-7 kcal/mol
Surface area16000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.410, 67.410, 179.791
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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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 / 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: Chemical ChemComp-D8U / deuterium(1+)


Mass: 2.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: D / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 100 mM HEPES pH=7.5 and 200 mM KCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12951N
22951N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-00711.542
SPALLATION SOURCEORNL Spallation Neutron Source MANDI22.00-4.16
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEOct 15, 2019
ORNL ANGER CAMERA2SCINTILLATIONSep 11, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.5421
221
34.161
Reflection

Biso Wilson estimate: 25.62 Å2 / Entry-ID: 9YZV

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Diffraction-IDNet I/σ(I)
1.63-48.963109299.86.70.991121.4
2.15-14.821234788.69.40.9529.7
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.63-1.6614940.8331
2.15-2.2312550.492

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
Refinement

SU ML: 0.1461 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 13.8879 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.63-33.13X-RAY DIFFRACTION43.070.15480.13340.1345158029474310545.0999.6111.35
2.15-14.09NEUTRON DIFFRACTION0.28130.23181234688.032
Refinement stepCycle: LAST / Resolution: 1.63→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1420 0 0 129 1549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113727
X-RAY DIFFRACTIONf_angle_d1.4626526
X-RAY DIFFRACTIONf_dihedral_angle_d20.647938
X-RAY DIFFRACTIONf_chiral_restr0.078253
X-RAY DIFFRACTIONf_plane_restr0.008667
NEUTRON DIFFRACTIONf_bond_d0.0113727
NEUTRON DIFFRACTIONf_angle_d1.4626526
NEUTRON DIFFRACTIONf_dihedral_angle_d20.647938
NEUTRON DIFFRACTIONf_chiral_restr0.078253
NEUTRON DIFFRACTIONf_plane_restr0.008667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.680.2251410.22692606X-RAY DIFFRACTION99
1.68-1.740.18221410.17312615X-RAY DIFFRACTION100
1.74-1.810.17941320.15812638X-RAY DIFFRACTION100
1.81-1.890.18911450.15682618X-RAY DIFFRACTION100
1.89-1.990.14291490.13892644X-RAY DIFFRACTION100
1.99-2.120.1551320.12452661X-RAY DIFFRACTION100
2.12-2.280.15441560.12412658X-RAY DIFFRACTION100
2.28-2.510.16721520.12132674X-RAY DIFFRACTION100
2.51-2.870.13571350.13112710X-RAY DIFFRACTION100
2.88-3.620.15131560.13372740X-RAY DIFFRACTION100
3.62-33.130.14991410.1282910X-RAY DIFFRACTION98
2.14-2.360.37531530.33252909NEUTRON DIFFRACTION90
2.36-2.690.3131710.27962905NEUTRON DIFFRACTION89
2.69-3.390.25841570.20962888NEUTRON DIFFRACTION87
3.39-14.090.19771420.14133021NEUTRON DIFFRACTION86
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4038-0.5349-0.53243.77320.44053.804-0.04490.1752-0.2699-0.1710.0141-0.15260.41540.1630.06290.29050.0187-0.01070.23910.01420.2298-18.17-23.735-16.8948
24.373-0.1015-0.7863.1599-0.84652.6282-0.12810.0076-0.64360.06430.05890.31140.654-0.37220.08140.3769-0.0746-0.01640.2820.03490.3035-27.4357-26.9044-12.2249
34.1023-0.68020.50664.384-0.82764.8131-0.0274-0.3338-0.4410.2420.09850.0040.62710.022-0.04970.36990.0458-0.02070.24210.07540.2501-16.4142-28.8171-3.8633
42.8932-1.51661.46057.0528-3.06225.9272-0.1289-0.3281-0.01870.58540.0628-0.41690.15120.50360.09210.28580.0911-0.06980.35560.00430.2543-6.7682-20.3821-0.037
54.1485-2.2186-2.34012.91850.53962.9653-0.01130.02470.0453-0.16750.0023-0.19020.18140.3586-0.02940.24460.01470.0040.2767-0.00560.2252-8.9609-16.2304-20.32
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 115 )
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 157 )
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 189 )

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