6XI1

Crystal structure of tetra-tandem repeat in extending RTX adhesin from Aeromonas hydrophila

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Essential role of calcium in extending RTX adhesins to their target.

Vance, T.D.R., Ye, Q., Conroy, B., Davies, P.L.

(2020) J Struct Biol X 4: 100036-100036

  • DOI: https://doi.org/10.1016/j.yjsbx.2020.100036
  • Primary Citation of Related Structures:  
    6XI1, 6XI3

  • PubMed Abstract: 

    • RTX adhesins are long, multi-domain proteins present on the outer membrane of many Gram-negative bacteria. From this vantage point, adhesins use their distal ligand-binding domains for surface attachment leading to biofilm formation. To expand the reach of the ligand-binding domains, RTX adhesins maintain a central extender region of multiple tandem repeats, which makes up most of the proteins' large molecular weight ...

    RTX adhesins are long, multi-domain proteins present on the outer membrane of many Gram-negative bacteria. From this vantage point, adhesins use their distal ligand-binding domains for surface attachment leading to biofilm formation. To expand the reach of the ligand-binding domains, RTX adhesins maintain a central extender region of multiple tandem repeats, which makes up most of the proteins' large molecular weight. Alignments of the 10-15-kDa extender domains show low sequence identity between adhesins. Here we have produced and structurally characterized protein constructs of four tandem repeats (tetra-tandemers) from two different RTX adhesins. In comparing the tetra-tandemers to each other and already solved structures from Marinomonas primoryensis and Salmonella enterica , the extender domains fold as diverse beta-sandwich structures with widely differing calcium contents. However, all the tetra-tandemers have at least one calcium ion coordinated in the linker region between beta-sandwich domains whose role appears to be the rigidification of the extender region to help the adhesin extend its reach.

    Organizational Affiliation: 

    Department of Biomedical and Molecular Science, Queen's University Kingston ON, Canada.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Flagellin hook IN motif familyA [auth AAA],
B [auth BBB]		449Aeromonas hydrophila subsp. hydrophila ATCC 7966Mutation(s): 0 
Gene Names: AHA_3491
UniProt
Find proteins for A0KNW4 (Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049))
Explore A0KNW4 
Go to UniProtKB:  A0KNW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0KNW4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG
Download Ideal Coordinates CCD File 
EA [auth BBB]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth BBB],
BA [auth BBB],
C [auth AAA],
CA [auth BBB],
D [auth AAA],
AA [auth BBB],
BA [auth BBB],
C [auth AAA],
CA [auth BBB],
D [auth AAA],
DA [auth BBB],
E [auth AAA],
F [auth AAA],
G [auth AAA],
H [auth AAA],
X [auth BBB],
Y [auth BBB],
Z [auth BBB]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
GA [auth BBB],
HA [auth BBB],
IA [auth BBB],
JA [auth BBB],
K [auth AAA],
GA [auth BBB],
HA [auth BBB],
IA [auth BBB],
JA [auth BBB],
K [auth AAA],
KA [auth BBB],
L [auth AAA],
LA [auth BBB],
M [auth AAA],
MA [auth BBB],
N [auth AAA],
NA [auth BBB],
O [auth AAA],
OA [auth BBB],
P [auth AAA],
PA [auth BBB],
Q [auth AAA],
QA [auth BBB],
R [auth AAA],
RA [auth BBB],
S [auth AAA],
SA [auth BBB],
T [auth AAA],
U [auth AAA],
V [auth AAA],
W [auth AAA]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
I [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
FA [auth BBB],
J [auth AAA]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.67α = 97.555
b = 50.37β = 98.244
c = 124.6γ = 101.719
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
PHENIXmodel building
BUCCANEERmodel building
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2016-04810

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release