- PDB-4c8d: Crystal structure of JmjC domain of human histone 3 Lysine-specif... -
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Basic information
Entry
Database: PDB / ID: 4c8d
Title
Crystal structure of JmjC domain of human histone 3 Lysine-specific demethylase 3B (KDM3B)
Components
LYSINE-SPECIFIC DEMETHYLASE 3B
Keywords
OXIDOREDUCTASE
Function / homology
Function and homology information
histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / antioxidant activity / histone deacetylase complex / transcription coregulator activity / HDMs demethylate histones / chromatin DNA binding / chromatin / regulation of transcription by RNA polymerase II ...histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / antioxidant activity / histone deacetylase complex / transcription coregulator activity / HDMs demethylate histones / chromatin DNA binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding Similarity search - Function
Histone demethylase JHDM2-like / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology
LYSINE-SPECIFICDEMETHYLASE3B / JMJC DOMAIN OF HUMAN HISTONE 3 LYSINE-SPECIFIC DEMETHYLASE 3 JMJC DOMAIN-CONTAINING HISTONE ...JMJC DOMAIN OF HUMAN HISTONE 3 LYSINE-SPECIFIC DEMETHYLASE 3 JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 2B / JUMONJI DOMAIN-CONTAINING PROTEIN 1B / NUCLEAR PROTEIN 5QNCA
Mass: 40278.543 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, RESIDUES 1380-1720 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q7LBC6, 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: 2.18→69.12 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.78 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23911
1110
5.1 %
RANDOM
Rwork
0.1943
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obs
0.19651
20691
97.96 %
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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