8C51

Trypanosoma brucei IMP dehydrogenase (cyto) crystallized in High Five cells revealing native ligands ATP, GDP and phosphate. Diffraction data collection at 100 K in cellulo


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst.

Schonherr, R.Boger, J.Lahey-Rudolph, J.M.Harms, M.Kaiser, J.Nachtschatt, S.Wobbe, M.Duden, R.Konig, P.Bourenkov, G.Schneider, T.R.Redecke, L.

(2024) Nat Commun 15: 1709-1709

  • DOI: https://doi.org/10.1038/s41467-024-45985-7
  • Primary Citation of Related Structures:  
    8C51, 8C53, 8C5K, 8CD4, 8CD5, 8CD6, 8CGX, 8CGY

  • PubMed Abstract: 

    With the advent of serial X-ray crystallography on microfocus beamlines at free-electron laser and synchrotron facilities, the demand for protein microcrystals has significantly risen in recent years. However, by in vitro crystallization extensive efforts are usually required to purify proteins and produce sufficiently homogeneous microcrystals. Here, we present InCellCryst, an advanced pipeline for producing homogeneous microcrystals directly within living insect cells. Our baculovirus-based cloning system enables the production of crystals from completely native proteins as well as the screening of different cellular compartments to maximize chances for protein crystallization. By optimizing cloning procedures, recombinant virus production, crystallization and crystal detection, X-ray diffraction data can be collected 24 days after the start of target gene cloning. Furthermore, improved strategies for serial synchrotron diffraction data collection directly from crystals within living cells abolish the need to purify the recombinant protein or the associated microcrystals.


  • Organizational Affiliation

    Institute of Biochemistry, University of Lübeck, Lübeck, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase
A, B
511Trypanosoma bruceiMutation(s): 0 
EC: 1.1.1.205
UniProt
Find proteins for P50098 (Trypanosoma brucei brucei)
Explore P50098 
Go to UniProtKB:  P50098
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50098
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.75α = 90
b = 205.75β = 90
c = 92.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
CrystFELdata reduction
CrystFELdata scaling
Cootmodel building
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany05K18FLA, InCellSX
Joachim Herz StiftungGermanyPhD scholarship
German Research Foundation (DFG)GermanyEXC306

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references