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Yorodumi- PDB-5fym: Crystal structure of JmjC domain of human histone demethylase UTY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fym | ||||||
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Title | Crystal structure of JmjC domain of human histone demethylase UTY in complex with D-2-hydroxyglutarate | ||||||
Components | HISTONE DEMETHYLASE UTY | ||||||
Keywords | OXIDOREDUCTASE / TCA INTERMEDIATE | ||||||
Function / homology | Function and homology information [histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / MLL3/4 complex / histone demethylase activity / HDMs demethylate histones / chromatin DNA binding / heart development / regulation of gene expression / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2- Hydroxyglutarate Authors: Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fym.cif.gz | 211 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fym.ent.gz | 166.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/5fym ftp://data.pdbj.org/pub/pdb/validation_reports/fy/5fym | HTTPS FTP |
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-Related structure data
Related structure data | 3zliS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 55006.402 Da / Num. of mol.: 2 / Fragment: JMJC DOMAIN, RESIDUES 878-1347 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: O14607, 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 |
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-Non-polymers , 5 types, 673 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: 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: 2.84 Å3/Da / Density % sol: 56.76 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: 0.1M HEPES PH 7.4, 0.2M TRIMETHYLAMINE N-OXIDE, 15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.82 Å / Num. obs: 79206 / % possible obs: 100 % / Observed criterion σ(I): 1.1 / Redundancy: 7.8 % / Biso Wilson estimate: 30.94 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZLI Resolution: 2→36.817 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 26.65 / 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→36.817 Å
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Refine LS restraints |
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LS refinement shell |
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