+Open data
-Basic information
Entry | Database: PDB / ID: 3sf8 | ||||||
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Title | Structural insights into thiol stabilization of DJ-1 | ||||||
Components | (Protein DJ-1) x 2 | ||||||
Keywords | ONCOPROTEIN / UNKNOWN FUNCTION / oxidative stress / redox regulation / cysteine oxidation / protecting DJ-1 oxidation / reduced DJ-1 / class I glutamine amidotransferase family / cytoprotective activity against oxidative stress / Cysteine sulfenic acid modification / HYDROLASE | ||||||
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, methylglyoxal removal / glutathione deglycation / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate ...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, methylglyoxal removal / glutathione deglycation / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal 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 protein K48-linked deubiquitination / negative regulation of ubiquitin-specific protease activity / protein deglycation, glyoxal removal / glycolate biosynthetic process / guanine deglycation, glyoxal removal / glyoxal metabolic process / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / guanine deglycation / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / oxidoreductase activity, acting on peroxide as acceptor / protein deglycase activity / positive regulation of acute inflammatory response to antigenic stimulus / positive regulation of dopamine biosynthetic process / superoxide dismutase copper chaperone activity / positive regulation of NAD(P)H oxidase activity / positive regulation of autophagy of mitochondrion / lactate biosynthetic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular detoxification of aldehyde / positive regulation of superoxide dismutase activity / small protein activating enzyme binding / Hydrolases; Acting on ester bonds; Thioester hydrolases / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of ubiquitin-protein transferase activity / peroxiredoxin activity / detoxification of copper ion / negative regulation of protein acetylation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of transcription regulatory region DNA binding / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of androgen receptor activity / membrane hyperpolarization / protein deglycosylation / negative regulation of protein sumoylation / oxygen sensor activity / regulation of androgen receptor signaling pathway / negative regulation of protein export from nucleus / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / cupric ion binding / ubiquitin-like protein conjugating enzyme binding / insulin secretion / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / dopamine uptake involved in synaptic transmission / positive regulation of reactive oxygen species biosynthetic process / nuclear androgen receptor binding / hydrogen peroxide metabolic process / ubiquitin-specific protease binding / cytokine binding / cuprous ion binding / single fertilization / membrane depolarization / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / negative regulation of protein ubiquitination / activation of protein kinase B activity / mitochondrion organization / adult locomotory behavior / SUMOylation of transcription cofactors / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / negative regulation of protein binding / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein-containing complex assembly / adherens junction / Late endosomal microautophagy / negative regulation of protein kinase activity / mitochondrial intermembrane space / PML body / cellular response to hydrogen peroxide / autophagy Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Premkumar, L. / Dobaczewska, M.K. / Riedl, S.J. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: Identification of an artificial peptide motif that binds and stabilizes reduced human DJ-1. Authors: Premkumar, L. / Dobaczewska, M.K. / Riedl, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sf8.cif.gz | 160.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sf8.ent.gz | 128 KB | Display | PDB format |
PDBx/mmJSON format | 3sf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/3sf8 ftp://data.pdbj.org/pub/pdb/validation_reports/sf/3sf8 | HTTPS FTP |
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-Related structure data
Related structure data | 1pdvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20175.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Production host: Escherichia coli (E. coli) References: UniProt: Q99497, Hydrolases; Acting on peptide bonds (peptidases) |
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#2: Protein | Mass: 20159.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Production host: Escherichia coli (E. coli) References: UniProt: Q99497, Hydrolases; Acting on peptide bonds (peptidases) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.37 % |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: 45% (v/v) polyproylene glycol 400, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 3, 2011 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→20 Å / Num. obs: 47218 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.53→1.61 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 4.7 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PDV Resolution: 1.56→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.058 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.6 Å / Total num. of bins used: 20
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