5NM3

Deinococcus radiodurans BphP PAS-GAF-PHY Y263F mutant, pre-illuminated

Summary for 5NM3

Related5NFX
DescriptorBacteriophytochrome, 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid (3 entities in total)
Functional Keywordskinase, photosensor, transferase, phytochrome
Biological sourceDeinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Total number of polymer chains4
Total molecular weight228602.79
Authors
Takala, H.,Westehoff, S.,Ihalainen, J.A. (deposition date: 2017-04-05, release date: 2018-04-18, Last modification date: 2018-06-06)
Primary citation
Takala, H.,Lehtivuori, H.K.,Berntsson, O.,Hughes, A.,Nanekar, R.,Niebling, S.,Panman, M.,Henry, L.,Menzel, A.,Westenhoff, S.,Ihalainen, J.A.
On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome.
J. Biol. Chem., 293:8161-8172, 2018
PubMed: 29622676 (PDB entries with the same primary citation)
DOI: 10.1074/jbc.RA118.001794
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3.3 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.26330.1%1.1%2.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5nm3
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Molmil generated image of 5nm3
rotated about x axis by 90°
Molmil generated image of 5nm3
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5nm3
no rotation
Molmil generated image of 5nm3
rotated about x axis by 90°
Molmil generated image of 5nm3
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5nm3.pdb2.gz [156.23 KB])
Coordinate files for Biological unit (5nm3.pdb1.gz [158.45 KB])