DNA (5'-D(*TP*TP*CP*TP*CP*TP*GP*TP*TP*TP*TP*G)-3')
Lysine-specific demethylase REF6
Keywords
DNA BINDING PROTEIN/DNA / REF6 / zinc finger / 5mC / DNA complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information
regulation of ethylene-activated signaling pathway / abscisic acid catabolic process / release of seed from dormancy / positive regulation of lateral root development / response to diterpene / heat acclimation / protein localization to heterochromatin / response to brassinosteroid / sugar mediated signaling pathway / unidimensional cell growth ...regulation of ethylene-activated signaling pathway / abscisic acid catabolic process / release of seed from dormancy / positive regulation of lateral root development / response to diterpene / heat acclimation / protein localization to heterochromatin / response to brassinosteroid / sugar mediated signaling pathway / unidimensional cell growth / regulation of photoperiodism, flowering / systemic acquired resistance / vegetative to reproductive phase transition of meristem / ethylene-activated signaling pathway / histone H3K27me2/H3K27me3 demethylase activity / leaf development / 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 / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / response to abscisic acid / Ino80 complex / abscisic acid-activated signaling pathway / epigenetic regulation of gene expression / response to mechanical stimulus / protein homooligomerization / : / response to heat / sequence-specific DNA binding / positive regulation of gene expression / regulation of DNA-templated transcription / nucleus / metal ion binding Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / zinc finger / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger C2H2 type domain profile. ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / zinc finger / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type Similarity search - Domain/homology
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / DNA / DNA (> 10) / Lysine-specific demethylase REF6 Similarity search - Component
Lysine-specificdemethylaseREF6 / Jumonji domain-containing protein 12 / Lysine-specific histone demethylase REF6 / Protein RELATIVE ...Jumonji domain-containing protein 12 / Lysine-specific histone demethylase REF6 / Protein RELATIVE OF EARLY FLOWERING 6
Mass: 12026.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: REF6, JMJ12, PKDM9A, At3g48430, T29H11_50 / Production host: Escherichia coli (E. coli) References: UniProt: Q9STM3, 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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DNA chain , 2 types, 2 molecules DC
#2: DNA chain
DNA (5'-D(*TP*TP*CP*TP*CP*TP*GP*TP*TP*TP*TP*G)-3')
Mass: 3625.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*A)-3')
Mass: 3384.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.888 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24923
810
4.9 %
RANDOM
Rwork
0.20488
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-
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obs
0.20701
15643
99.84 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å