Loading
PDBj
メニューPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help

5PHH

PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09457a

5PHH の概要
エントリーDOI10.2210/pdb5phh/pdb
Group depositionPanDDA analysis group deposition of models with modelled events (e.g. bound ligands) (G_1002020)
分子名称Lysine-specific demethylase 4D, ZINC ION, NICKEL (II) ION, ... (8 entities in total)
機能のキーワードpandda, sgc - diamond i04-1 fragment screening, jmj domain, epigenetics, oxidoreductase
由来する生物種Homo sapiens (Human)
細胞内の位置Nucleus : Q6B0I6
タンパク質・核酸の鎖数1
化学式量合計43231.57
構造登録者
主引用文献Pearce, N.M.,Krojer, T.,Bradley, A.R.,Collins, P.,Nowak, R.P.,Talon, R.,Marsden, B.D.,Kelm, S.,Shi, J.,Deane, C.M.,von Delft, F.
A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Nat Commun, 8:15123-15123, 2017
Cited by
PubMed Abstract: In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous ('weak' or 'noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state-even from inaccurate maps-by subtracting a proportion of the confounding 'ground state'; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches.
PubMed: 28436492
DOI: 10.1038/ncomms15123
主引用文献が同じPDBエントリー
実験手法
X-RAY DIFFRACTION (1.604 Å)
構造検証レポート
Validation report summary of 5phh
検証レポート(詳細版)ダウンロードをダウンロード

229183

件を2024-12-18に公開中

PDB statisticsPDBj update infoContact PDBjnumon