8PXL

Structure of NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4, solved at wavelength 1.37 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


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Literature

Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.

El Omari, K.Duman, R.Mykhaylyk, V.Orr, C.M.Latimer-Smith, M.Winter, G.Grama, V.Qu, F.Bountra, K.Kwong, H.S.Romano, M.Reis, R.I.Vogeley, L.Vecchia, L.Owen, C.D.Wittmann, S.Renner, M.Senda, M.Matsugaki, N.Kawano, Y.Bowden, T.A.Moraes, I.Grimes, J.M.Mancini, E.J.Walsh, M.A.Guzzo, C.R.Owens, R.J.Jones, E.Y.Brown, D.G.Stuart, D.I.Beis, K.Wagner, A.

(2023) Commun Chem 6: 219-219

  • DOI: https://doi.org/10.1038/s42004-023-01014-0
  • Primary Citation of Related Structures:  
    8PWN, 8PX0, 8PX1, 8PX4, 8PX5, 8PX7, 8PX9, 8PXC, 8PXG, 8PXH, 8PXJ, 8PXK, 8PXL, 8PYV, 8PYZ, 8PZ4, 8PZ5

  • PubMed Abstract: 

    Despite recent advances in cryo-electron microscopy and artificial intelligence-based model predictions, a significant fraction of structure determinations by macromolecular crystallography still requires experimental phasing, usually by means of single-wavelength anomalous diffraction (SAD) techniques. Most synchrotron beamlines provide highly brilliant beams of X-rays of between 0.7 and 2 Å wavelength. Use of longer wavelengths to access the absorption edges of biologically important lighter atoms such as calcium, potassium, chlorine, sulfur and phosphorus for native-SAD phasing is attractive but technically highly challenging. The long-wavelength beamline I23 at Diamond Light Source overcomes these limitations and extends the accessible wavelength range to λ = 5.9 Å. Here we report 22 macromolecular structures solved in this extended wavelength range, using anomalous scattering from a range of elements which demonstrate the routine feasibility of lighter atom phasing. We suggest that, in light of its advantages, long-wavelength crystallography is a compelling option for experimental phasing.


  • Organizational Affiliation

    Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin reductase408Pseudomonas sp. KKS102Mutation(s): 0 
Gene Names: bphA4
UniProt
Find proteins for Q52437 (Pseudomonas sp. (strain KKS102))
Explore Q52437 
Go to UniProtKB:  Q52437
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ52437
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.243α = 90
b = 98.243β = 90
c = 170.476γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Diamond Light SourceUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release