5Y5L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.

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.

(2017) Nat Commun 8: 1585-1585

  • DOI: https://doi.org/10.1038/s41467-017-01702-1
  • Primary Citation of Related Structures:  
    5Y5F, 5Y5G, 5Y5H, 5Y5I, 5Y5J, 5Y5K, 5Y5L, 5Y5M

  • PubMed Abstract: 

    Time-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers a crystallographic method to track enzymatic reactions. Here we demonstrate the application of this method using fungal NO reductase, a heme-containing enzyme, at room temperature. Twenty milliseconds after caged-NO photolysis, we identify a NO-bound form of the enzyme, which is an initial intermediate with a slightly bent Fe-N-O coordination geometry at a resolution of 2.1 Å. The NO geometry is compatible with those analyzed by XFEL-based cryo-crystallography and QM/MM calculations, indicating that we obtain an intact Fe 3+ -NO coordination structure that is free of X-ray radiation damage. The slightly bent NO geometry is appropriate to prevent immediate NO dissociation and thus accept H - from NADH. The combination of using XFEL and a caged-compound is a powerful tool for determining functional enzyme structures during catalytic reactions at the atomic level.


  • Organizational Affiliation

    Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan. yshiro@sci.u-hyogo.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADP nitrous oxide-forming nitric oxide reductase
A, B
403Fusarium oxysporumMutation(s): 0 
Gene Names: CYP55A1CYP55
EC: 1.7.1.14
UniProt
Find proteins for P23295 (Fusarium oxysporum)
Explore P23295 
Go to UniProtKB:  P23295
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23295
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.6α = 90
b = 102.3β = 92.6
c = 73.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-11-22
    Changes: Refinement description