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Yorodumi- PDB-3zli: Crystal structure of JmjC domain of human histone demethylase UTY -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zli | ||||||
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Title | Crystal structure of JmjC domain of human histone demethylase UTY | ||||||
Components | HISTONE DEMETHYLASE UTY | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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 / 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: 1.8 Å | ||||||
Authors | Vollmar, M. / Gileadi, C. / Shrestha, L. / Goubin, S. / Johansson, C. / Krojer, T. / Raynor, J.W. / Bradley, A. / von Delft, F. / Arrowsmith, C.H. ...Vollmar, M. / Gileadi, C. / Shrestha, L. / Goubin, S. / Johansson, C. / Krojer, T. / Raynor, J.W. / Bradley, A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Human Uty(Kdm6C) is a Male-Specific Nepsilon-Methyl Lysyl Demethylase. Authors: Walport, L.J. / Hopkinson, R.J. / Vollmar, M. / Madden, S.K. / Gileadi, C. / Oppermann, U. / Schofield, C.J. / Johansson, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zli.cif.gz | 374.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zli.ent.gz | 305.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/3zli ftp://data.pdbj.org/pub/pdb/validation_reports/zl/3zli | HTTPS FTP |
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-Related structure data
Related structure data | 3zpoC 3avsS 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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2 |
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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) / Plasmid: PFB-CT10HF-LIC / 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, 569 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #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: 2.69 Å3/Da / Density % sol: 54.31 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2M TRIMETHYLAMINE N-OXIDE; 0.1M HEPES PH 7.5; 10%(W/V) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→49.96 Å / Num. obs: 110147 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AVS Resolution: 1.8→50.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.5 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.803 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50.01 Å
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Refine LS restraints |
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