+Open data
-Basic information
Entry | Database: PDB / ID: 5fbj | ||||||
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Title | Complex structure of JMJD5 and substrate | ||||||
Components | Lysine-specific demethylase 8 | ||||||
Keywords | OXIDOREDUCTASE / Histone enzyme | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | Liu, H.L. / Wang, Y. / Wang, C. / Zhang, G.Y. | ||||||
Citation | Journal: To Be Published Title: to be published Authors: Liu, H.L. / Wang, Y. / Wang, C. / Dai, S.D. / Zhang, G.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fbj.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fbj.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 5fbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/5fbj ftp://data.pdbj.org/pub/pdb/validation_reports/fb/5fbj | HTTPS FTP |
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-Related structure data
Related structure data | 4qu1S 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: 27318.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM8, JMJD5 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8N371, [histone H3]-dimethyl-L-lysine36 demethylase |
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#2: Chemical | ChemComp-AKG / |
#3: Chemical | ChemComp-NMM / ( |
#4: Chemical | ChemComp-ZN / |
#5: 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: 2.3 Å3/Da / Density % sol: 46.49 % |
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Crystal grow | Temperature: 281 K / Method: evaporation / Details: PEG3350 HEPEPS-Na / PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→38.975 Å / Num. obs: 7775 / % possible obs: 77.24 % / Redundancy: 6.7 % / Net I/σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QU1 Resolution: 2.42→38.975 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.07 / 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 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→38.975 Å
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Refine LS restraints |
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LS refinement shell |
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