5Y5J

Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state)

Summary for 5Y5J

DescriptorNADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, GLYCEROL, ... (4 entities in total)
Functional Keywordsmetal-binding, oxidoreductase
Biological sourceFusarium oxysporum (Fusarium vascular wilt)
Total number of polymer chains2
Total molecular weight90258.54
Authors
Primary citation
Tosha, T.,Nomura, T.,Nishida, T.,Saeki, N.,Okubayashi, K.,Yamagiwa, R.,Sugahara, M.,Nakane, T.,Yamashita, K.,Hirata, K.,Ueno, G.,Kimura, T.,Hisano, T.,Muramoto, K.,Sawai, H.,Takeda, H.,Mizohata, E.,Yamashita, A.,Kanematsu, Y.,Takano, Y.,Nango, E.,Tanaka, R.,Nureki, O.,Shoji, O.,Ikemoto, Y.,Murakami, H.,Owada, S.,Tono, K.,Yabashi, M.,Yamamoto, M.,Ago, H.,Iwata, S.,Sugimoto, H.,Shiro, Y.,Kubo, M.
Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8:1585-1585, 2017
PubMed: 29147002 (PDB entries with the same primary citation)
DOI: 10.1038/s41467-017-01702-1
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.20430.1%0.3%1.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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More Biological unit images

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(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5y5j.pdb2.gz [73.2 KB])
Coordinate files for Biological unit (5y5j.pdb1.gz [70.99 KB])