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- PDB-1q2u: Crystal structure of DJ-1/RS and implication on familial Parkinso... -

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Basic information

Entry
Database: PDB / ID: 1q2u
TitleCrystal structure of DJ-1/RS and implication on familial Parkinson's disease
ComponentsRNA-binding protein regulatory subunit
KeywordsRNA BINDING PROTEIN / Breast cancer / Parkinson's disease / male fertility / protein inhibitor of activated STAT / androgen receptor
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 / negative regulation of protein acetylation / 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 / 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 / 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 / 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 / cuprous ion binding / regulation of synaptic vesicle endocytosis / 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 / positive regulation of peptidyl-serine phosphorylation / 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 / 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 / cellular response to hydrogen peroxide / kinase binding / 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 (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 / MAD / Resolution: 1.6 Å
AuthorsHuai, Q. / Sun, Y. / Wang, H. / Chin, L.S. / Li, L. / Robinson, H. / Ke, H.
CitationJournal: Febs Lett. / Year: 2003
Title: Crystal structure of DJ-1/RS and implication on familial Parkinson's disease
Authors: Huai, Q. / Sun, Y. / Wang, H. / Chin, L.S. / Li, L. / Robinson, H. / Ke, H.
History
DepositionJul 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
SupersessionJul 28, 2009ID: 1PS4
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein regulatory subunit


Theoretical massNumber of molelcules
Total (without water)19,9171
Polymers19,9171
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: RNA-binding protein regulatory subunit

A: RNA-binding protein regulatory subunit


Theoretical massNumber of molelcules
Total (without water)39,8342
Polymers39,8342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area2690 Å2
ΔGint-16 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.233, 75.233, 75.311
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RNA-binding protein regulatory subunit / DJ-1


Mass: 19917.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DJ-1 / Plasmid: pET3E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(codonplus) / References: UniProt: Q99497
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% PEG 3350, 0.1M Tris.base, 5% MPD, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
220 mMTris1droppH7.5
350 mM1dropNaCl
41 mMEDTA1drop
51 mMbeta-mercaptoethanol1drop
612 %PEG33501reservoir
70.1 MTris1reservoirpH8.5
85 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.979 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→99 Å / Num. all: 33002 / Num. obs: 33002 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.4
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 5 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 337226
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 100 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.6→99 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3179 -random
Rwork0.191 ---
all-32945 --
obs-31910 96.9 %-
Displacement parametersBiso mean: 16 Å2
Baniso -1Baniso -2Baniso -3
1--1.578 Å2-0.818 Å20 Å2
2---1.578 Å20 Å2
3---3.156 Å2
Refinement stepCycle: LAST / Resolution: 1.6→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 0 195 1586
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_mcangle_it1.1592
X-RAY DIFFRACTIONc_mcbond_it0.6591.5
X-RAY DIFFRACTIONc_scangle_it1.6812.5
X-RAY DIFFRACTIONc_scbond_it1.0772
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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