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Yorodumi- PDB-5a1f: Crystal structure of the catalytic domain of PLU1 in complex with... -
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-Basic information
Entry | Database: PDB / ID: 5a1f | ||||||
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Title | Crystal structure of the catalytic domain of PLU1 in complex with N-oxalylglycine. | ||||||
Components | LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B | ||||||
Keywords | OXIDOREDUCTASE / LYSINE-SPECIFIC DEMETHYLASE 5B | ||||||
Function / homology | Function and homology information regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus ...regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus / branching involved in mammary gland duct morphogenesis / single fertilization / histone demethylase activity / response to fungicide / cellular response to leukemia inhibitory factor / post-embryonic development / Chromatin modifications during the maternal to zygotic transition (MZT) / HDMs demethylate histones / transcription corepressor activity / rhythmic process / sequence-specific double-stranded DNA binding / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Srikannathasan, V. / Johansson, C. / Strain-Damerell, C. / Gileadi, C. / Szykowska, A. / Kupinska, K. / Kopec, J. / Krojer, T. / Steuber, H. / von Delft, F. ...Srikannathasan, V. / Johansson, C. / Strain-Damerell, C. / Gileadi, C. / Szykowska, A. / Kupinska, K. / Kopec, J. / Krojer, T. / Steuber, H. / von Delft, F. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Oppermann, U. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development. Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, ...Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, A. / Steuber, H. / Egner, U. / Badock, V. / Munro, S. / Lathangue, N.B. / Westaway, S. / Brown, J. / Athanasou, N. / Prinjha, R. / Brennan, P.E. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a1f.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a1f.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 5a1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/5a1f ftp://data.pdbj.org/pub/pdb/validation_reports/a1/5a1f | HTTPS FTP |
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-Related structure data
Related structure data | 4uf0C 5a3pC 5a3tC 5a3wC 5fpuC 5fpvC 5funC 5fupC 5fv3C 5fwjC 4gioS S: Starting model for refinement C: citing same article (ref.) |
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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: 54986.094 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, RESIDUES, JMJC DOMAIN, RESIDUES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Gene: KDM5B, JARID1B, PLU1, RBBP2H1 / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q9UGL1, 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 ...References: UniProt: Q9UGL1, 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, 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 , 7 types, 218 molecules
#2: Chemical | #3: Chemical | ChemComp-OGA / | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Chemical | ChemComp-EPE / | #7: Chemical | ChemComp-EDO / #8: 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: 4.18 Å3/Da / Density % sol: 70.37 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.1M HEPES PH 8.0, 0.8M POTASSIUM PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.91742 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91742 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→19.77 Å / Num. obs: 52970 / % possible obs: 100 % / Observed criterion σ(I): 2.6 / Redundancy: 11.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.14 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 2.42 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GIO Resolution: 2.1→50.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.166 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY SOME SIDE CHAINS REMOVED AND SOME OF THE RESIDUES HAVE ALTERNATIVE CONFIRMATION.
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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: 47.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50.01 Å
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Refine LS restraints |
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