Petrobactin-binding engineered lipocalin without ligand

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Reprogramming Human Siderocalin To Neutralize Petrobactin, the Essential Iron Scavenger of Anthrax Bacillus.

Dauner, M.Eichinger, A.Lucking, G.Scherer, S.Skerra, A.

(2018) Angew Chem Int Ed Engl 57: 14619-14623

  • DOI: https://doi.org/10.1002/anie.201807442
  • Primary Citation of Related Structures:  
    6GQZ, 6GR0

  • PubMed Abstract: 

    Bacillus anthracis owes its pronounced virulence-apart from specific toxins-to a twofold import mechanism for Fe III ions. This pathogenic bacterium secretes the siderophores bacillibactin (BB) and petrobactin (PB), of which only BB is neutralized by human siderocalin, an abundant lipocalin in plasma. We describe its reshaping via combinatorial protein design to bind PB⋅Fe III instead of BB⋅Fe III , and with even higher affinity (K D ≈20 pm). X-ray crystallographic analysis of the resulting "petrocalin" in complex with PB⋅Ga III reveals a positively charged ligand pocket while the extended butterfly-like conformation of the bound PB provides a rationale for the missing recognition by the natural siderocalin. In microbiological studies, a combination of petrocalin and siderocalin effectively suppressed the growth of a BB + /PB + strain of Bacillus cereus under iron-limiting culture conditions. Thus, our reprogrammed lipocalin may offer novel treatment options for devastating infections caused by B. anthracis.

  • Organizational Affiliation

    Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutrophil gelatinase-associated lipocalin
A, B
174Homo sapiensMutation(s): 25 
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens)
Explore P80188 
Go to UniProtKB:  P80188
PHAROS:  P80188
GTEx:  ENSG00000148346 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80188
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.140 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.99α = 90
b = 65.95β = 96.77
c = 67.94γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description