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Yorodumi- PDB-5fjk: Crystal structure of human JMJD2C catalytic domain in complex 6-e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fjk | ||||||
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Title | Crystal structure of human JMJD2C catalytic domain in complex 6-ethyl- 5-methyl-7-oxo-4,7-dihydropyrazolo(1,5-a)pyrimidine-3-carbonitrile | ||||||
Components | LYSINE-SPECIFIC DEMETHYLASE 4C | ||||||
Keywords | OXIDOREDUCTASE / TRANSCRIPTION REGULATION / METAL BINDING / DEMETHYLASE / 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 / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Cecatiello, V. / Pasqualato, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structures of Human Jmjd2C Catalytic Domain Bound to Inhibitors Authors: Cecatiello, V. / Pasqualato, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fjk.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fjk.ent.gz | 126 KB | Display | PDB format |
PDBx/mmJSON format | 5fjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fjk_validation.pdf.gz | 458.9 KB | Display | wwPDB validaton report |
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Full document | 5fjk_full_validation.pdf.gz | 460.6 KB | Display | |
Data in XML | 5fjk_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 5fjk_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/5fjk ftp://data.pdbj.org/pub/pdb/validation_reports/fj/5fjk | HTTPS FTP |
-Related structure data
Related structure data | 5fjhC 2xmlS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40517.246 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 3-347 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): PLYSS 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 , 6 types, 362 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-NI / | ||||
#4: Chemical | ChemComp-EM6 / | ||||
#5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.94 % / Description: NONE |
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Crystal grow | pH: 7.25 Details: 21% PEG 3350, 5% 1,2 ETHANEDIOL, 0.2 M NANO3, 0.1 M BIS-TRIS PROPANE PH 7.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→53.77 Å / Num. obs: 48173 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 20.82 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.66→1.7 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.5 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XML Resolution: 1.66→53.774 Å / SU ML: 0.17 / σ(F): 1.36 / Phase error: 22.58 / 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: 1.66→53.774 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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