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- PDB-3cza: Crystal Structure of E18D DJ-1 -

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Basic information

Entry
Database: PDB / ID: 3cza
TitleCrystal Structure of E18D DJ-1
ComponentsProtein DJ-1
KeywordsUNKNOWN FUNCTION / REACTIVE CYSTEINE / CHAPERONE / NUCLEUS / ONCOGENE / OXIDATION / PARKINSON DISEASE
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 / : / detection of oxidative stress / : / guanine deglycation, glyoxal removal / cellular detoxification of methylglyoxal ...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 / : / detection of oxidative stress / : / 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 / : / 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 / glyoxal metabolic process / guanine deglycation / detoxification of mercury ion / ubiquitin-protein transferase inhibitor activity / protein deglycase / hydrogen peroxide metabolic process / mercury ion binding / methylglyoxal metabolic 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 dopamine biosynthetic process / 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 / peroxiredoxin activity / cellular detoxification of aldehyde / 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 / negative regulation of protein export from nucleus / negative regulation of protein sumoylation / androgen receptor signaling pathway / cupric ion binding / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of androgen receptor signaling pathway / insulin secretion / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / oxygen sensor activity / single fertilization / nuclear androgen receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / ubiquitin-specific protease binding / cytokine binding / cuprous ion binding / signaling receptor activator activity / regulation of synaptic vesicle endocytosis / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / removal of superoxide radicals / negative regulation of protein ubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / SUMOylation of transcription cofactors / regulation of neuron apoptotic process / regulation of mitochondrial membrane potential / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / mitochondrion organization / adherens junction / positive regulation of protein-containing complex assembly / positive regulation of protein localization to nucleus / Late endosomal microautophagy / mitochondrial intermembrane space / PML body / positive regulation of reactive oxygen species metabolic process / cellular response to hydrogen peroxide / kinase binding / enzyme activator activity / autophagy / Chaperone Mediated Autophagy / Aggrephagy / glucose homeostasis / peptidase activity / synaptic vesicle / cellular response to oxidative stress / regulation of inflammatory response / response to oxidative stress / cell body / scaffold protein binding / negative regulation of neuron apoptotic process / DNA-binding transcription factor binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Ras protein signal transduction / transcription coactivator activity / protein stabilization / cadherin binding
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
MALONIC ACID / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsWitt, A.C. / Lakshminarasimhan, M. / Remington, B.C. / Hashim, S. / Pozharski, E. / Wilson, M.A.
CitationJournal: Biochemistry / Year: 2008
Title: Cysteine pKa depression by a protonated glutamic acid in human DJ-1.
Authors: Witt, A.C. / Lakshminarasimhan, M. / Remington, B.C. / Hasim, S. / Pozharski, E. / Wilson, M.A.
History
DepositionApr 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0782
Polymers20,9741
Non-polymers1041
Water3,981221
1
A: Protein DJ-1
hetero molecules

A: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1564
Polymers41,9482
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3020 Å2
ΔGint-28.4 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.826, 74.826, 74.777
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-1185-

HOH

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Components

#1: Protein Protein DJ-1 / Oncogene DJ-1


Mass: 20974.180 Da / Num. of mol.: 1 / Mutation: E18D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99497
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M sodium citrate, 50 mM HEPES, 10 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2006 / Details: BENT 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: 1.2→24 Å / Num. all: 75880 / Num. obs: 75880 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 35.5
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.9 / Num. unique all: 7498 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1P5F

1p5f


Resolution: 1.2→24 Å / Num. parameters: 15063 / Num. restraintsaints: 19045 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1637 3796 5 %RANDOM
Rwork0.1305 ---
obs0.1305 75840 99.9 %-
all-75840 --
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 1401 / Occupancy sum non hydrogen: 1595.5
Refinement stepCycle: LAST / Resolution: 1.2→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 0 7 221 1597
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0287
X-RAY DIFFRACTIONs_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.091
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.048
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.117
LS refinement shellResolution: 1.2→1.24 Å /
RfactorNum. reflection
Rwork0.259 -
obs-7018

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