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- PDB-4p36: Crystal structure of DJ-1 With Zn(II) bound (crystal 2) -

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Basic information

Entry
Database: PDB / ID: 4p36
TitleCrystal structure of DJ-1 With Zn(II) bound (crystal 2)
ComponentsProtein DJ-1
KeywordsHYDROLASE / Parkinson's disease / Oxidation
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
2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.182 Å
AuthorsTashiro, S. / Wu, C.-X. / Hoang, Q.Q. / Caaveiro, J.M.M. / Tsumoto, K.
CitationJournal: Biochemistry / Year: 2014
Title: Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1.
Authors: Tashiro, S. / Caaveiro, J.M. / Wu, C.X. / Hoang, Q.Q. / Tsumoto, K.
History
DepositionMar 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Jul 23, 2014Group: Structure summary
Revision 1.3Sep 23, 2015Group: Other
Revision 1.4Nov 22, 2017Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list ...diffrn_source / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.5Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.6Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2953
Polymers19,9331
Non-polymers3622
Water4,179232
1
A: Protein DJ-1
hetero molecules

A: Protein DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5906
Polymers39,8662
Non-polymers7244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area2950 Å2
ΔGint-94 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.015, 75.015, 75.525
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 DJ1 / Parkinson disease protein 7


Mass: 19933.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q99497, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28O7
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM Sodium citrate 30% (v:v) PEG-400 500 uM Zinc sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→29.9 Å / Num. obs: 80469 / % possible obs: 99.9 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.2
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementResolution: 1.182→29.84 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 12.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1384 2417 3.01 %
Rwork0.1187 --
obs0.1193 80429 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.182→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 21 232 1629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071620
X-RAY DIFFRACTIONf_angle_d1.2842220
X-RAY DIFFRACTIONf_dihedral_angle_d14.346694
X-RAY DIFFRACTIONf_chiral_restr0.07261
X-RAY DIFFRACTIONf_plane_restr0.007289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.182-1.20640.27771350.21844515X-RAY DIFFRACTION100
1.2064-1.23260.18621400.16754544X-RAY DIFFRACTION100
1.2326-1.26130.15671270.14714548X-RAY DIFFRACTION100
1.2613-1.29280.16071380.13564546X-RAY DIFFRACTION100
1.2928-1.32780.16461580.12774554X-RAY DIFFRACTION100
1.3278-1.36690.14651390.11224545X-RAY DIFFRACTION100
1.3669-1.4110.15251290.1044547X-RAY DIFFRACTION100
1.411-1.46140.14151310.09994581X-RAY DIFFRACTION100
1.4614-1.51990.13271540.09324579X-RAY DIFFRACTION100
1.5199-1.58910.10951330.08874568X-RAY DIFFRACTION100
1.5891-1.67290.09341360.08924587X-RAY DIFFRACTION100
1.6729-1.77770.10481390.0964580X-RAY DIFFRACTION100
1.7777-1.91490.11371310.10514621X-RAY DIFFRACTION100
1.9149-2.10760.12831520.10924593X-RAY DIFFRACTION100
2.1076-2.41240.11891530.11144638X-RAY DIFFRACTION100
2.4124-3.03890.15161580.1254658X-RAY DIFFRACTION100
3.0389-29.84910.14991640.13444808X-RAY DIFFRACTION100

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