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- PDB-1p5f: Crystal Structure of Human DJ-1 -

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Basic information

Entry
Database: PDB / ID: 1p5f
TitleCrystal Structure of Human DJ-1
ComponentsRNA-binding protein regulatory subunit
KeywordsUNKNOWN FUNCTION
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 / AB INITIO PHASING / Resolution: 1.1 Å
AuthorsWilson, M.A. / Collins, J.L. / Hod, Y. / Ringe, D. / Petsko, G.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: The 1.1 A resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease
Authors: Wilson, M.A. / Collins, J.L. / Hod, Y. / Ringe, D. / Petsko, G.A.
History
DepositionApr 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 14, 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
Water4,540252
1
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 operation4_556y,x,-z+11
Buried area2680 Å2
ΔGint-17 kcal/mol
Surface area14800 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.306, 75.306, 75.422
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-398-

HOH

DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: y, x, -z+1

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Components

#1: Protein RNA-binding protein regulatory subunit


Mass: 19917.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99497
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.33 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 400, tris-HCl, sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 23K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
123 mg/mlprotein1drop
230 %PEG4001reservoir
3100 mMTris-HCl1reservoirpH8.5
4200 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 29, 2002 / Details: CONICAL SI MIRROR
RadiationMonochromator: BENT GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.1→33 Å / Num. all: 99689 / Num. obs: 99689 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 36.4
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.6 / Num. unique all: 9597 / % possible all: 95.8
Reflection
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 33 Å / Num. obs: 100971
Reflection shell
*PLUS
% possible obs: 95.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
SHELXmodel building
SHELXL-97refinement
RESOLVEphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→33 Å / Num. parameters: 15913 / Num. restraintsaints: 21047 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1609 4714 4.7 %RANDOM
Rwork0.1393 ---
all0.1393 99689 --
obs0.1393 99689 99.4 %-
Refine analyzeNum. disordered residues: 18 / Occupancy sum hydrogen: 1392.6 / Occupancy sum non hydrogen: 1551.6
Refinement stepCycle: LAST / Resolution: 1.1→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 0 252 1622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.075
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0.103
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 33 Å / Rfactor Rfree: 0.161 / Rfactor Rwork: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.031
X-RAY DIFFRACTIONs_chiral_restr0.084

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