6U57

KDO8PS Structure Determined at the EuXFEL using Segmented Flow Injection

  • Classification: TRANSFERASE
  • Organism(s): Escherichia coli BL21(DE3)
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-08-27 Released: 2020-09-02 
  • Deposition Author(s): Botha, S., Ros, A.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Segmented flow generator for serial crystallography at the European X-ray free electron laser.

Echelmeier, A.Cruz Villarreal, J.Messerschmidt, M.Kim, D.Coe, J.D.Thifault, D.Botha, S.Egatz-Gomez, A.Gandhi, S.Brehm, G.Conrad, C.E.Hansen, D.T.Madsen, C.Bajt, S.Meza-Aguilar, J.D.Oberthur, D.Wiedorn, M.O.Fleckenstein, H.Mendez, D.Knoska, J.Martin-Garcia, J.M.Hu, H.Lisova, S.Allahgholi, A.Gevorkov, Y.Ayyer, K.Aplin, S.Ginn, H.M.Graafsma, H.Morgan, A.J.Greiffenberg, D.Klujev, A.Laurus, T.Poehlsen, J.Trunk, U.Mezza, D.Schmidt, B.Kuhn, M.Fromme, R.Sztuk-Dambietz, J.Raab, N.Hauf, S.Silenzi, A.Michelat, T.Xu, C.Danilevski, C.Parenti, A.Mekinda, L.Weinhausen, B.Mills, G.Vagovic, P.Kim, Y.Kirkwood, H.Bean, R.Bielecki, J.Stern, S.Giewekemeyer, K.Round, A.R.Schulz, J.Dorner, K.Grant, T.D.Mariani, V.Barty, A.Mancuso, A.P.Weierstall, U.Spence, J.C.H.Chapman, H.N.Zatsepin, N.Fromme, P.Kirian, R.A.Ros, A.

(2020) Nat Commun 11: 4511-4511

  • DOI: https://doi.org/10.1038/s41467-020-18156-7
  • Primary Citation of Related Structures:  
    6U57

  • PubMed Abstract: 

    Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.


  • Organizational Affiliation

    Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-dehydro-3-deoxyphosphooctonate aldolase284Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: kdsAECBD_2406
EC: 2.5.1.55
UniProt
Find proteins for P0A715 (Escherichia coli (strain K12))
Explore P0A715 
Go to UniProtKB:  P0A715
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A715
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.192 
  • Space Group: I 2 3
  • Diffraction Data: https://doi.org/10.11577/1660970
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118α = 90
b = 118β = 90
c = 118γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
CrystFELdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1231306
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM095583
German Research Foundation (DFG)Germany390715994

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-11
    Changes: Refinement description