6HCP | pdb_00006hcp

Crystal structure of BauA, the Ferric preacinetobactin receptor from Acinetobacter baumannii

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 
    0.177 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Preacinetobactin not acinetobactin is essential for iron uptake by the BauA transporter of the pathogenAcinetobacter baumannii.

Moynie, L., Serra, I., Scorciapino, M.A., Oueis, E., Page, M.G., Ceccarelli, M., Naismith, J.H.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.42270
  • Primary Citation Related Structures: 
    6H7F, 6H7V, 6HCP

  • PubMed Abstract: 

    New strategies are urgently required to develop antibiotics. The siderophore uptake system has attracted considerable attention, but rational design of siderophore antibiotic conjugates requires knowledge of recognition by the cognate outer-membrane transporter. Acinetobacter baumannii is a serious pathogen, which utilizes (pre)acinetobactin to scavenge iron from the host. We report the structure of the (pre)acinetobactin transporter BauA bound to the siderophore, identifying the structural determinants of recognition. Detailed biophysical analysis confirms that BauA recognises preacinetobactin. We show that acinetobactin is not recognised by the protein, thus preacinetobactin is essential for iron uptake. The structure shows and NMR confirms that under physiological conditions, a molecule of acinetobactin will bind to two free coordination sites on the iron preacinetobactin complex. The ability to recognise a heterotrimeric iron-preacinetobactin-acinetobactin complex may rationalize contradictory reports in the literature. These results open new avenues for the design of novel antibiotic conjugates (trojan horse) antibiotics.

    • Organizational Affiliation: 
    • Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Oxford, England.

Macromolecule Content 

  • Total Structure Weight: 244.27 kDa 
  • Atom Count: 18,809 
  • Modeled Residue Count: 2,013 
  • Deposited Residue Count: 2,118 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BauA
A, B, C
706Acinetobacter baumanniiMutation(s): 0 
Gene Names: bauA
Membrane Entity: Yes 
UniProt
Find proteins for Q76HJ9 (Acinetobacter baumannii)
Explore Q76HJ9 
Go to UniProtKB:  Q76HJ9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ76HJ9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8E

Query on C8E


Download:Ideal Coordinates CCD File
AD [auth C]
BD [auth C]
CA [auth A]
CD [auth C]
DA [auth A]
AD [auth C],
BD [auth C],
CA [auth A],
CD [auth C],
DA [auth A],
DD [auth C],
EA [auth A],
ED [auth C],
FA [auth A],
FD [auth C],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
LB [auth B],
MA [auth A],
MB [auth B],
NB [auth B],
OB [auth B],
PB [auth B],
QB [auth B],
RB [auth B],
SB [auth B],
SC [auth C],
TB [auth B],
TC [auth C],
UB [auth B],
UC [auth C],
VC [auth C],
WC [auth C],
XC [auth C],
YC [auth C],
ZC [auth C]
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
PO4

Query on PO4


Download:Ideal Coordinates CCD File
VB [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO


Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth B]
AC [auth C]
BA [auth A]
BB [auth B]
AA [auth A],
AB [auth B],
AC [auth C],
BA [auth A],
BB [auth B],
BC [auth C],
CB [auth B],
CC [auth C],
D [auth A],
DB [auth B],
DC [auth C],
E [auth A],
EB [auth B],
EC [auth C],
F [auth A],
FB [auth B],
FC [auth C],
G [auth A],
GB [auth B],
GC [auth C],
H [auth A],
HB [auth B],
HC [auth C],
I [auth A],
IB [auth B],
IC [auth C],
J [auth A],
JB [auth B],
JC [auth C],
K [auth A],
KB [auth B],
KC [auth C],
L [auth A],
LC [auth C],
M [auth A],
MC [auth C],
N [auth A],
NA [auth B],
NC [auth C],
O [auth A],
OA [auth B],
OC [auth C],
P [auth A],
PA [auth B],
PC [auth C],
Q [auth A],
QA [auth B],
QC [auth C],
R [auth A],
RA [auth B],
RC [auth C],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
U [auth A],
UA [auth B],
V [auth A],
VA [auth B],
W [auth A],
WA [auth B],
WB [auth C],
X [auth A],
XA [auth B],
XB [auth C],
Y [auth A],
YA [auth B],
YB [auth C],
Z [auth A],
ZA [auth B],
ZB [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free:  0.177 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.2α = 90
b = 219.52β = 99.21
c = 101.43γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references, Refinement description