6QWG

Serial Femtosecond Crystallography Structure of Cu Nitrite Reductase from Achromobacter cycloclastes: Nitrite complex at Room Temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 

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Literature

High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography.

Moreno-Chicano, T.Ebrahim, A.Axford, D.Appleby, M.V.Beale, J.H.Chaplin, A.K.Duyvesteyn, H.M.E.Ghiladi, R.A.Owada, S.Sherrell, D.A.Strange, R.W.Sugimoto, H.Tono, K.Worrall, J.A.R.Owen, R.L.Hough, M.A.

(2019) IUCrJ 6: 1074-1085

  • DOI: 10.1107/S2052252519011655
  • Primary Citation of Related Structures:  
    6I7C, 6I6G, 6I7F, 6QWG

  • PubMed Abstract: 
  • High-throughput X-ray crystal structures of protein-ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallogra ...

    High-throughput X-ray crystal structures of protein-ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein-ligand complexes using SFX.


    Organizational Affiliation

    School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper-containing nitrite reductaseA333Achromobacter cycloclastesMutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
Find proteins for P25006 (Achromobacter cycloclastes)
Explore P25006 
Go to UniProtKB:  P25006
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NO2
Query on NO2

Download Ideal Coordinates CCD File 
A
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.6α = 90
b = 97.6β = 90
c = 97.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M022714/1
Leverhulme TrustUnited KingdomRPG-2014-0355

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release