Computational protocol: Studies on the Interaction of the Histone Demethylase KDM5B with Tricarboxylic Acid Cycle Intermediates

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Protocol publication

[…] A JmjN–JmjC linked construct of KDM5B (F26-K772) was crystallized using the sitting drop vapor diffusion method as previously described . Crystals of KDM5B were soaked with final concentrations of 10–25 mM of the TCA intermediates supplemented with 25% (v/v) ethylene glycol for 15 to 120 min and then flash frozen in liquid nitrogen. Data were collected at Diamond Light Source beamlines I04-1, I02 and I04. Data sets were processed using Xia2 , molecular replacement and initial refinement in DIMPLE pipeline (used the PDB ID: 5A1F as a model). Iterative model building was done using COOT and refinement with PHENIX and BUSTER v2.10.1 . Data collection and refinement statistics are given in Table S3, Supplementary Information. […]

Pipeline specifications

Software tools xia2, Coot, PHENIX
Application Protein structure analysis
Organisms Homo sapiens, Mus musculus
Diseases Neoplasms
Chemicals Esters, Pyruvic Acid, Succinic Acid, Oxaloacetic Acid