+Open data
-Basic information
Entry | Database: PDB / ID: 4xdo | ||||||
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Title | Crystal structure of human KDM4C catalytic domain with OGA | ||||||
Components | Lysine-specific demethylase 4CKDM4C | ||||||
Keywords | OXIDOREDUCTASE / LYSINE-SPECIFIC DEMETHYLASE 4C | ||||||
Function / homology | Function and homology information H3K9me3 modified histone binding / histone H3K36 demethylase activity / regulation of stem cell differentiation / blastocyst formation / regulation of androgen receptor signaling pathway / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / nuclear androgen receptor binding / stem cell population maintenance / androgen receptor signaling pathway ...H3K9me3 modified histone binding / histone H3K36 demethylase activity / regulation of stem cell differentiation / blastocyst formation / regulation of androgen receptor signaling pathway / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / nuclear androgen receptor binding / stem cell population maintenance / androgen receptor signaling pathway / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / nuclear receptor coactivator activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / regulation of gene expression / chromatin remodeling / positive regulation of cell population proliferation / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.97 Å | ||||||
Authors | Swinger, K.K. / Boriack-Sjodin, P.A. | ||||||
Citation | Journal: J Biomol Screen / Year: 2015 Title: A High-Throughput Mass Spectrometry Assay Coupled with Redox Activity Testing Reduces Artifacts and False Positives in Lysine Demethylase Screening. Authors: Wigle, T.J. / Swinger, K.K. / Campbell, J.E. / Scholle, M.D. / Sherrill, J. / Admirand, E.A. / Boriack-Sjodin, P.A. / Kuntz, K.W. / Chesworth, R. / Moyer, M.P. / Scott, M.P. / Copeland, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xdo.cif.gz | 163.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xdo.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/4xdo ftp://data.pdbj.org/pub/pdb/validation_reports/xd/4xdo | HTTPS FTP |
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-Related 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: 39406.035 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 10-347) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4C, GASC1, JHDM3C, JMJD2C, KIAA0780 / Production host: Escherichia coli (E. coli) References: UniProt: Q9H3R0, 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, 387 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-PG4 / | #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: 2.62 Å3/Da / Density % sol: 52.99 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.8 M Lithium chloride, 0.1 M Tris pH 8.5, 28 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å | |||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.97→40.8 Å / Num. obs: 57310 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.054 / Net I/σ(I): 12 / Num. measured all: 240106 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 1.97→40.58 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9 / SU B: 4.405 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 101.39 Å2 / Biso mean: 24.476 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 1.97→40.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.021 Å / Total num. of bins used: 20
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