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Yorodumi- PDB-3uyj: Crystal structure of JMJD5 catalytic core domain in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uyj | ||||||
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Title | Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG | ||||||
Components | Lysine-specific demethylase 8 | ||||||
Keywords | OXIDOREDUCTASE / jellyroll-like all beta fold / Demethylase / Nuclear | ||||||
Function / homology | Function and homology information [protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle / p53 binding / chromosome / fibroblast proliferation / endopeptidase activity / in utero embryonic development / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / proteolysis / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.351 Å | ||||||
Authors | Su, X. / Li, H. | ||||||
Citation | Journal: To be Published Title: Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG Authors: Su, X. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uyj.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uyj.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 3uyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/3uyj ftp://data.pdbj.org/pub/pdb/validation_reports/uy/3uyj | 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: 28683.609 Da / Num. of mol.: 2 / Fragment: Catalytic core domain, UNP residues 173-416 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD5, KDM8 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta2(DE3) References: UniProt: Q8N371, [histone H3]-dimethyl-L-lysine36 demethylase #2: Chemical | #3: Chemical | #4: 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: 3.14 Å3/Da / Density % sol: 60.81 % |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 7.5 Details: 8% PEG3350, 0.1M HepesNa pH 7.5, EVAPORATION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97922 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2011 / Details: mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→20 Å / Num. all: 31174 / Num. obs: 30809 / % possible obs: 98.83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 42.86 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.335 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.351→19.994 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 0 / Phase error: 25.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.602 Å2 / ksol: 0.385 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.351→19.994 Å
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Refine LS restraints |
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LS refinement shell |
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