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Yorodumi- PDB-1ucf: The Crystal Structure of DJ-1, a Protein Related to Male Fertilit... -
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-Basic information
Entry | Database: PDB / ID: 1ucf | ||||||
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Title | The Crystal Structure of DJ-1, a Protein Related to Male Fertility and Parkinson's Disease | ||||||
Components | RNA-binding protein regulatory subunit | ||||||
Keywords | RNA BINDING PROTEIN / FLAVODOXIN-LIKE ROSSMANN FOLD | ||||||
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 / MIR / Resolution: 1.95 Å | ||||||
Authors | Honbou, K. / Suzuki, N.N. / Horiuchi, M. / Niki, T. / Taira, T. / Ariga, H. / Inagaki, F. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2003 Title: The Crystal Structure of DJ-1, a Protein Related to Male Fertility and Parkinson's Disease Authors: Honbou, K. / Suzuki, N.N. / Horiuchi, M. / Niki, T. / Taira, T. / Ariga, H. / Inagaki, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ucf.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ucf.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ucf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/1ucf ftp://data.pdbj.org/pub/pdb/validation_reports/uc/1ucf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19917.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DJ-1 / Plasmid: pGEX-6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q99497 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: sodium citrate, HEPES, DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 16, 2001 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. all: 34488 / Num. obs: 34488 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.073 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.399 / % possible all: 93.8 |
Reflection | *PLUS Num. measured all: 145149 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.95→37.52 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 128474.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.27 Å2 / ksol: 0.367766 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→37.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.194 / Rfactor Rwork: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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