6GR0

Petrobactin-binding engineered lipocalin in complex with gallium-petrobactin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neutrophil gelatinase-associated lipocalinA, B, C174Homo sapiensMutation(s): 25 
Gene Names: LCN2HNLNGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens)
Explore P80188 
Go to UniProtKB:  P80188
PHAROS:  P80188
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80188
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F8W
Query on F8W

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
H [auth B],
I [auth B],
L [auth C],
D [auth A],
F [auth B],
H [auth B],
I [auth B],
L [auth C],
N [auth C]
4-[4-[3-[[3,4-bis(oxidanyl)phenyl]carbonylamino]propylamino]butylamino]-2-[2-[4-[3-[[3,4-bis(oxidanyl)phenyl]carbonylamino]propylamino]butylamino]-2-oxidanylidene-ethyl]-2-oxidanyl-4-oxidanylidene-butanoic acid
C34 H50 N6 O11
GKIMOVAPSAVJHZ-UHFFFAOYSA-N
 Ligand Interaction
GA
Query on GA

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth B],
K [auth B],
M [auth C],
E [auth A],
G [auth B],
J [auth B],
K [auth B],
M [auth C],
O [auth C],
P [auth C]
GALLIUM (III) ION
Ga
CKHJYUSOUQDYEN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
F8W Binding MOAD:  6GR0 Kd: 0.09 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.336α = 90
b = 112.17β = 90
c = 124.849γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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