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- PDB-3cyf: Crystal Structure of E18N DJ-1 -

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Basic information

Entry
Database: PDB / ID: 3cyf
TitleCrystal Structure of E18N DJ-1
ComponentsProtein DJ-1
KeywordsUNKNOWN FUNCTION / REACTIVE CYSTEINE / CHAPERONE / NUCLEUS / ONCOGENE / OXIDATION / PARKINSON DISEASE
Function / homology
Function and homology information


tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, glyoxal removal / protein deglycation, methylglyoxal removal / : / detoxification of hydrogen peroxide ...tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, glyoxal removal / protein deglycation, methylglyoxal removal / : / 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 pyrroline-5-carboxylate reductase activity / positive regulation of tyrosine 3-monooxygenase activity / positive regulation of L-dopa biosynthetic process / positive regulation of L-dopa decarboxylase activity / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / glyoxalase (glycolic acid-forming) activity / negative regulation of ubiquitin-specific protease activity / negative regulation of protein K48-linked deubiquitination / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / positive regulation of NAD(P)H oxidase activity / glycolate biosynthetic process / detection of oxidative stress / glyoxal metabolic process / guanine deglycation / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / protein deglycase activity / oxidoreductase activity, acting on peroxide as acceptor / positive regulation of dopamine biosynthetic process / positive regulation of autophagy of mitochondrion / superoxide dismutase copper chaperone activity / positive regulation of acute inflammatory response to antigenic stimulus / positive regulation of superoxide dismutase activity / lactate biosynthetic process / : / cellular detoxification of aldehyde / protein deglycosylation / positive regulation of transcription regulatory region DNA binding / small protein activating enzyme binding / peroxiredoxin activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of ubiquitin-protein transferase activity / detoxification of copper ion / negative regulation of protein acetylation / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of androgen receptor activity / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of protein sumoylation / membrane hyperpolarization / negative regulation of protein export from nucleus / regulation of androgen receptor signaling pathway / cupric ion binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / insulin secretion / ubiquitin-like protein conjugating enzyme binding / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / oxygen sensor activity / hydrogen peroxide metabolic process / nuclear androgen receptor binding / positive regulation of reactive oxygen species biosynthetic process / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / cuprous ion binding / cytokine binding / 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 / activation of protein kinase B activity / adult locomotory behavior / SUMOylation of transcription cofactors / negative regulation of protein phosphorylation / negative regulation of protein binding / regulation of mitochondrial membrane potential / positive regulation of interleukin-8 production / mitochondrion organization / negative regulation of extrinsic apoptotic signaling pathway / adherens junction / positive regulation of DNA-binding transcription factor activity / negative regulation of protein kinase activity / Late endosomal microautophagy / positive regulation of protein-containing complex assembly / PML body / mitochondrial intermembrane space / kinase 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
Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWitt, A.C. / Lakshminarasimhan, M. / Remington, B.C. / Hasim, 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 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Other
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein DJ-1


Theoretical massNumber of molelcules
Total (without water)21,0051
Polymers21,0051
Non-polymers00
Water3,279182
1
A: Protein DJ-1

A: Protein DJ-1


Theoretical massNumber of molelcules
Total (without water)42,0102
Polymers42,0102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2680 Å2
ΔGint-19.6 kcal/mol
Surface area14780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.025, 75.025, 75.054
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 Protein DJ-1 / Oncogene DJ-1


Mass: 21005.193 Da / Num. of mol.: 1 / Mutation: E18N
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6 M sodium citrate, 50 mM HEPES, 10 mM DTT, pH 8.0, 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 (Rh COATED)
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: 1.6→30 Å / Num. all: 32697 / Num. obs: 32697 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 5.1 / Num. unique all: 3216 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1P5F

1p5f


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.117 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18353 1656 5.1 %RANDOM
Rwork0.15848 ---
all0.15973 32639 --
obs0.15973 32639 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.857 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.11 Å20 Å2
2--0.21 Å20 Å2
3----0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.068 Å0.066 Å
Luzzati sigma a-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 0 182 1553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221446
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9971963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58625.6653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27215260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.271157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021074
X-RAY DIFFRACTIONr_nbd_refined0.2580.2728
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.215
X-RAY DIFFRACTIONr_mcbond_it2.6132991
X-RAY DIFFRACTIONr_mcangle_it3.24931544
X-RAY DIFFRACTIONr_scbond_it3.8292498
X-RAY DIFFRACTIONr_scangle_it6.5493419
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 130 -
Rwork0.193 2209 -
obs-2339 98.44 %

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