- PDB-6a58: Structure of histone demethylase REF6 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6a58
Title
Structure of histone demethylase REF6
Components
Lysine-specific demethylase REF6
Keywords
DNA BINDING PROTEIN / Complex / histone demethylase REF6 / DNA / zinc finger
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 / response to abscisic acid / Ino80 complex / abscisic acid-activated signaling pathway / response to mechanical stimulus / epigenetic regulation of gene expression / protein homooligomerization / response to heat / sequence-specific DNA binding / regulation of DNA-templated transcription / positive regulation of gene expression / 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
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: 16521.723 Da / Num. of mol.: 1 / Fragment: Ig gamma-1 chain C region 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
Resolution: 1.57→50 Å / Num. obs: 23425 / % possible obs: 99.7 % / Redundancy: 12.8 % / Rsym value: 0.057 / Net I/σ(I): 76.8
Reflection shell
Resolution: 1.57→1.6 Å / Num. unique obs: 1174 / Rsym value: 0.496 / % possible all: 99.1
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0189
refinement
HKL-2000
datareduction
HKL-2000
datascaling
HKL2Map
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.57→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.614 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23384
1187
5.1 %
RANDOM
Rwork
0.21085
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obs
0.21199
22150
99.71 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å