+Open data
-Basic information
Entry | Database: PDB / ID: 8wug | ||||||
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Title | The Crystal Structure of JMJD2D from Biortus. | ||||||
Components | Lysine-specific demethylase 4D | ||||||
Keywords | OXIDOREDUCTASE / Chromatin regulator / Dioxygenase / Transcription / Transcription regulation / Iron / Metal-binding / Zinc | ||||||
Function / homology | Function and homology information positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / regulation of protein phosphorylation / double-strand break repair via homologous recombination ...positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / regulation of protein phosphorylation / double-strand break repair via homologous recombination / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / inflammatory response / chromatin remodeling / chromatin / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: The Crystal Structure of JMJD2D from Biortus. Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wug.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wug.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 8wug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wug_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 8wug_full_validation.pdf.gz | 456.3 KB | Display | |
Data in XML | 8wug_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 8wug_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/8wug ftp://data.pdbj.org/pub/pdb/validation_reports/wu/8wug | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39491.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4D / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B0I6 |
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-Non-polymers , 6 types, 428 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | ChemComp-PEG / | ||||
#5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M HEPES, NaOH pH 7.5, 2% PEG 400, 2M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.89 Å / Num. obs: 40301 / % possible obs: 92 % / Redundancy: 15.9 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 60.6 |
Reflection shell | Resolution: 1.7→1.74 Å / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 13.4 / Num. unique obs: 2235 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.887 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.161 / SU B: 1.543 / SU ML: 0.053 / Average fsc free: 0.9766 / Average fsc work: 0.9837 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.096 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.554 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→47.887 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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