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PDBsum entry 5pnh
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Oxidoreductase
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PDB id
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5pnh
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PDB id:
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| Name: |
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Oxidoreductase
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Title:
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Pandda analysis group deposition -- crystal structure of jmjd2d after initial refinement with no ligand modelled (structure 211)
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Structure:
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Lysine-specific demethylase 4d. Chain: a. Synonym: jmjc domain-containing histone demethylation protein 3d, jumonji domain-containing protein 2d. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: kdm4d, jhdm3d, jmjd2d. Expressed in: escherichia coli. Expression_system_taxid: 562
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Resolution:
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1.14Å
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R-factor:
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0.183
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R-free:
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0.205
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Authors:
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N.M.Pearce,T.Krojer,R.Talon,A.R.Bradley,M.Fairhead,R.Sethi,N.Wright, E.Maclean,P.Collins,J.Brandao-Neto,A.Douangamath,Z.Renjie,A.Dias, M.Vollmar,J.Ng,A.Szykowska,N.Burgess-Brown,P.E.Brennan,O.Cox, U.Oppermann,C.Bountra,C.H.Arrowsmith,A.Edwards,F.Von Delft
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Key ref:
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N.M.Pearce
et al.
(2017).
A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Nat Commun,
8,
15123.
PubMed id:
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Date:
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07-Feb-17
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Release date:
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15-Mar-17
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PROCHECK
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Headers
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References
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Q6B0I6
(KDM4D_HUMAN) -
Lysine-specific demethylase 4D from Homo sapiens
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Seq:
Struc:
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523 a.a.
331 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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Enzyme class:
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E.C.1.14.11.66
- [histone H3]-trimethyl-L-lysine(9) demethylase.
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Reaction:
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N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 2 2-oxoglutarate + 2 O2 = N6-methyl-L-lysyl9-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2
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N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3]
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+
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2
×
2-oxoglutarate
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+
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2
×
O2
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=
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N(6)-methyl-L-lysyl(9)-[histone H3]
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+
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2
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formaldehyde
Bound ligand (Het Group name = )
matches with 50.00% similarity
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+
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2
×
succinate
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+
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2
×
CO2
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Nat Commun
8:15123
(2017)
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PubMed id:
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A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
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N.M.Pearce,
T.Krojer,
A.R.Bradley,
P.Collins,
R.P.Nowak,
R.Talon,
B.D.Marsden,
S.Kelm,
J.Shi,
C.M.Deane,
F.von Delft.
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ABSTRACT
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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.
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