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Yorodumi- PDB-3n9o: ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K9me2 pep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n9o | ||||||
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Title | ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K9me2 peptide and NOG | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Histone / methylation / demethylase / PHD / JmjC / Fe(II) and alpha-KG (alpha-ketoglutarate)-dependent dioxygenase family | ||||||
Function / homology | Function and homology information HDMs demethylate histones / histone H3K27me2/H3K27me3 demethylase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / histone H3K9 demethylase activity / histone demethylase activity / methylated histone binding / transcription coregulator activity / structural constituent of chromatin / nucleosome / histone binding ...HDMs demethylate histones / histone H3K27me2/H3K27me3 demethylase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / histone H3K9 demethylase activity / histone demethylase activity / methylated histone binding / transcription coregulator activity / structural constituent of chromatin / nucleosome / histone binding / protein heterodimerization activity / regulation of transcription by RNA polymerase II / DNA binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.309 Å | ||||||
Authors | Yang, Y. / Hu, L. / Wang, P. / Hou, H. / Chen, C.D. / Xu, Y. | ||||||
Citation | Journal: Cell Res. / Year: 2010 Title: Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans Authors: Yang, Y. / Hu, L. / Wang, P. / Hou, H. / Lin, Y. / Liu, Y. / Li, Z. / Gong, R. / Feng, X. / Zhou, L. / Zhang, W. / Dong, Y. / Yang, H. / Lin, H. / Wang, Y. / Chen, C.D. / Xu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n9o.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n9o.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 3n9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/3n9o ftp://data.pdbj.org/pub/pdb/validation_reports/n9/3n9o | HTTPS FTP |
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-Related structure data
Related structure data | 3n9lC 3n9mSC 3n9nC 3n9pC 3n9qC C: citing same article (ref.) 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61945.496 Da / Num. of mol.: 1 / Fragment: PHD domain, UNP residues 201-724 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: F29B9.2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9GYI0, [histone H3]-dimethyl-L-lysine36 demethylase |
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-Protein/peptide , 2 types, 2 molecules BC
#2: Protein/peptide | Mass: 1607.877 Da / Num. of mol.: 1 / Fragment: JMJC domain, UNP residues 2-16 / Source method: obtained synthetically / Details: chemical synthesis, purchased from a company / Source: (synth.) Caenorhabditis elegans (invertebrata) / References: UniProt: P08898 |
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#3: Protein/peptide | Mass: 1847.152 Da / Num. of mol.: 1 / Fragment: JMJC domain, UNP residues 2-18 / Source method: obtained synthetically / Details: chemical synthesis, purchased from a company / Source: (synth.) Caenorhabditis elegans (invertebrata) / References: UniProt: P08898 |
-Non-polymers , 4 types, 281 molecules
#4: Chemical | ChemComp-FE2 / | ||||
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#5: Chemical | #6: Chemical | ChemComp-OGA / | #7: 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: 2.37 Å3/Da / Density % sol: 48.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 16% PEG 3350, 0.2M Sodium Fluoride, 0.1M Bis-Tris or HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.2828 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 6, 2009 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2828 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 27497 / % possible obs: 98.4 % / Biso Wilson estimate: 39.49 Å2 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3N9M Resolution: 2.309→44.28 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8261 / SU ML: 0.69 / σ(F): 1.35 / Phase error: 24.13 / 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: 37.574 Å2 / ksol: 0.331 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.72 Å2 / Biso mean: 44.6602 Å2 / Biso min: 18.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.309→44.28 Å
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Refine LS restraints |
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LS refinement shell |
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