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Structure paper

TitleCapturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Journal, issue, pagesNat Commun, Vol. 8, Page 1585-1585, Year 2017
Publish dateAug 9, 2017 (structure data deposition date)
AuthorsTosha, T. / Nomura, T. / Nishida, T. / Saeki, N. / Okubayashi, K. / Yamagiwa, R. / Sugahara, M. / Nakane, T. / Yamashita, K. / Hirata, K. ...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.
External linksNat Commun / PubMed:29147002
MethodsX-ray diffraction
Resolution1.36 - 2.1 Å
Structure data

PDB-5y5f:
Structure of cytochrome P450nor in NO-bound state: damaged by low-dose (0.72 MGy) X-ray
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-5y5g:
Structure of cytochrome P450nor in NO-bound state: damaged by high-dose (5.7 MGy) X-ray
Method: X-RAY DIFFRACTION / Resolution: 1.36 Å

PDB-5y5h:
SF-ROX structure of cytochrome P450nor (NO-bound state) determined at SACLA
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-5y5i:
Time-resolved SFX structure of cytochrome P450nor: 20 ms after photo-irradiation of caged NO in the presence of NADH (NO-bound state), light data
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-5y5j:
Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state)
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-5y5k:
Time-resolved SFX structure of cytochrome P450nor : 20 ms after photo-irradiation of caged NO in the absence of NADH (NO-bound state), light data
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-5y5l:
Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the absence of NADH (resting state)
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-5y5m:
SFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state)
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

Chemicals

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

ChemComp-NO:
NITRIC OXIDE

ChemComp-GOL:
GLYCEROL

ChemComp-HOH:
WATER

Source
  • fusarium oxysporum (fungus)
KeywordsOXIDOREDUCTASE / metal-binding

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