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Yorodumi- PDB-2ypd: Crystal structure of the Jumonji domain of human Jumonji domain c... -
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-Basic information
Entry | Database: PDB / ID: 2ypd | ||||||
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Title | Crystal structure of the Jumonji domain of human Jumonji domain containing 1C protein | ||||||
Components | PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN 2C | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information 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 / nuclear thyroid hormone receptor binding / dioxygenase activity / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / chromatin DNA binding / blood coagulation / Factors involved in megakaryocyte development and platelet production / chromatin ...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 / nuclear thyroid hormone receptor binding / dioxygenase activity / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / chromatin DNA binding / blood coagulation / Factors involved in megakaryocyte development and platelet production / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Vollmar, M. / Johansson, C. / Krojer, T. / Berridge, G. / Burgess-Brown, N. / Strain-Damerell, C. / Froese, S. / Williams, E. / Goubin, S. / Coutandin, D. ...Vollmar, M. / Johansson, C. / Krojer, T. / Berridge, G. / Burgess-Brown, N. / Strain-Damerell, C. / Froese, S. / Williams, E. / Goubin, S. / Coutandin, D. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein Authors: Vollmar, M. / Johansson, C. / Krojer, T. / Strain-Damerell, C. / Froese, S. / Williams, E. / Coutandin, D. / von Delft, F. / Weigelt, J. / 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 | 2ypd.cif.gz | 265.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ypd.ent.gz | 223.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ypd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/2ypd ftp://data.pdbj.org/pub/pdb/validation_reports/yp/2ypd | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45190.605 Da / Num. of mol.: 2 / Fragment: JUMONJI DOMAIN, RESIDUES 2157-2540 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q15652, 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 #2: Chemical | ChemComp-EMT / #3: Chemical | #4: 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: 2.26 Å3/Da / Density % sol: 45.72 % / Description: NONE |
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Crystal grow | Details: 13% PEG3350, 200 MM SODIUM MALONATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9736 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9736 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→92.82 Å / Num. obs: 50717 / % possible obs: 100 % / Observed criterion σ(I): 1.7 / Redundancy: 15.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.1→92.82 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.356 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.643 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→92.82 Å
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