6XI1 | pdb_00006xi1

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

PDB DOI: https://doi.org/10.2210/pdb6XI1/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Aeromonas hydrophila subsp. hydrophila ATCC 7966
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-06-19 Released: 2020-10-14
Deposition Author(s): Ye, Q., Vance, T.D.R., Conroy, B., Davies, P.L.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.210 (Depositor), 0.223 (DCC)
R-Value Work:
0.181 (Depositor), 0.196 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.1 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

PubMed: 32984811 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.yjsbx.2020.100036
Primary Citation 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. 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.

Macromolecule Content

Total Structure Weight: 93.01 kDa
Atom Count: 7,100
Modeled Residue Count: 851
Deposited Residue Count: 898
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellin hook IN motif family	A [auth AAA], B [auth BBB]	449	Aeromonas hydrophila subsp. hydrophila ATCC 7966	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0KNW4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain EA [auth BBB] MOL2 format, chain EA [auth BBB] mmCIF format, chain EA [auth BBB]	EA [auth BBB]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth BBB] Interactions & Density Focus chain EA [auth BBB]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth BBB] SDF format, chain BA [auth BBB] SDF format, chain C [auth AAA] SDF format, chain CA [auth BBB] SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain X [auth BBB] SDF format, chain Z [auth BBB] SDF format, chain Y [auth BBB] SDF format, chain DA [auth BBB] SDF format, chain D [auth AAA] MOL2 format, chain AA [auth BBB] MOL2 format, chain BA [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain CA [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain X [auth BBB] MOL2 format, chain Z [auth BBB] MOL2 format, chain Y [auth BBB] MOL2 format, chain DA [auth BBB] MOL2 format, chain D [auth AAA] mmCIF format, chain AA [auth BBB] mmCIF format, chain BA [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain CA [auth BBB] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain X [auth BBB] mmCIF format, chain Z [auth BBB] mmCIF format, chain Y [auth BBB] mmCIF format, chain DA [auth BBB] mmCIF format, chain D [auth AAA]	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		Interactions Focus chain AA [auth BBB] Focus chain BA [auth BBB] Focus chain C [auth AAA] Focus chain CA [auth BBB] Focus chain D [auth AAA] Focus chain DA [auth BBB] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain X [auth BBB] Focus chain Y [auth BBB] Focus chain Z [auth BBB] Interactions & Density Focus chain AA [auth BBB] Focus chain BA [auth BBB] Focus chain C [auth AAA] Focus chain CA [auth BBB] Focus chain D [auth AAA] Focus chain DA [auth BBB] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain X [auth BBB] Focus chain Y [auth BBB] Focus chain Z [auth BBB]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain GA [auth BBB] SDF format, chain HA [auth BBB] SDF format, chain IA [auth BBB] SDF format, chain JA [auth BBB] SDF format, chain K [auth AAA] SDF format, chain L [auth AAA] SDF format, chain LA [auth BBB] SDF format, chain M [auth AAA] SDF format, chain MA [auth BBB] SDF format, chain N [auth AAA] SDF format, chain NA [auth BBB] SDF format, chain O [auth AAA] SDF format, chain OA [auth BBB] SDF format, chain P [auth AAA] SDF format, chain PA [auth BBB] SDF format, chain Q [auth AAA] SDF format, chain QA [auth BBB] SDF format, chain R [auth AAA] SDF format, chain RA [auth BBB] SDF format, chain S [auth AAA] SDF format, chain SA [auth BBB] SDF format, chain T [auth AAA] SDF format, chain U [auth AAA] SDF format, chain W [auth AAA] SDF format, chain V [auth AAA] SDF format, chain KA [auth BBB] MOL2 format, chain GA [auth BBB] MOL2 format, chain HA [auth BBB] MOL2 format, chain IA [auth BBB] MOL2 format, chain JA [auth BBB] MOL2 format, chain K [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain LA [auth BBB] MOL2 format, chain M [auth AAA] MOL2 format, chain MA [auth BBB] MOL2 format, chain N [auth AAA] MOL2 format, chain NA [auth BBB] MOL2 format, chain O [auth AAA] MOL2 format, chain OA [auth BBB] MOL2 format, chain P [auth AAA] MOL2 format, chain PA [auth BBB] MOL2 format, chain Q [auth AAA] MOL2 format, chain QA [auth BBB] MOL2 format, chain R [auth AAA] MOL2 format, chain RA [auth BBB] MOL2 format, chain S [auth AAA] MOL2 format, chain SA [auth BBB] MOL2 format, chain T [auth AAA] MOL2 format, chain U [auth AAA] MOL2 format, chain W [auth AAA] MOL2 format, chain V [auth AAA] MOL2 format, chain KA [auth BBB] mmCIF format, chain GA [auth BBB] mmCIF format, chain HA [auth BBB] mmCIF format, chain IA [auth BBB] mmCIF format, chain JA [auth BBB] mmCIF format, chain K [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain LA [auth BBB] mmCIF format, chain M [auth AAA] mmCIF format, chain MA [auth BBB] mmCIF format, chain N [auth AAA] mmCIF format, chain NA [auth BBB] mmCIF format, chain O [auth AAA] mmCIF format, chain OA [auth BBB] mmCIF format, chain P [auth AAA] mmCIF format, chain PA [auth BBB] mmCIF format, chain Q [auth AAA] mmCIF format, chain QA [auth BBB] mmCIF format, chain R [auth AAA] mmCIF format, chain RA [auth BBB] mmCIF format, chain S [auth AAA] mmCIF format, chain SA [auth BBB] mmCIF format, chain T [auth AAA] mmCIF format, chain U [auth AAA] mmCIF format, chain W [auth AAA] mmCIF format, chain V [auth AAA] mmCIF format, chain KA [auth BBB]	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		Interactions Focus chain GA [auth BBB] Focus chain HA [auth BBB] Focus chain IA [auth BBB] Focus chain JA [auth BBB] Focus chain K [auth AAA] Focus chain KA [auth BBB] Focus chain L [auth AAA] Focus chain LA [auth BBB] Focus chain M [auth AAA] Focus chain MA [auth BBB] Focus chain N [auth AAA] Focus chain NA [auth BBB] Focus chain O [auth AAA] Focus chain OA [auth BBB] Focus chain P [auth AAA] Focus chain PA [auth BBB] Focus chain Q [auth AAA] Focus chain QA [auth BBB] Focus chain R [auth AAA] Focus chain RA [auth BBB] Focus chain S [auth AAA] Focus chain SA [auth BBB] Focus chain T [auth AAA] Focus chain U [auth AAA] Focus chain V [auth AAA] Focus chain W [auth AAA] Interactions & Density Focus chain GA [auth BBB] Focus chain HA [auth BBB] Focus chain IA [auth BBB] Focus chain JA [auth BBB] Focus chain K [auth AAA] Focus chain KA [auth BBB] Focus chain L [auth AAA] Focus chain LA [auth BBB] Focus chain M [auth AAA] Focus chain MA [auth BBB] Focus chain N [auth AAA] Focus chain NA [auth BBB] Focus chain O [auth AAA] Focus chain OA [auth BBB] Focus chain P [auth AAA] Focus chain PA [auth BBB] Focus chain Q [auth AAA] Focus chain QA [auth BBB] Focus chain R [auth AAA] Focus chain RA [auth BBB] Focus chain S [auth AAA] Focus chain SA [auth BBB] Focus chain T [auth AAA] Focus chain U [auth AAA] Focus chain V [auth AAA] Focus chain W [auth AAA]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth AAA] MOL2 format, chain I [auth AAA] mmCIF format, chain I [auth AAA]	I [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth AAA] Interactions & Density Focus chain I [auth AAA]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth AAA] SDF format, chain FA [auth BBB] MOL2 format, chain J [auth AAA] MOL2 format, chain FA [auth BBB] mmCIF format, chain J [auth AAA] mmCIF format, chain FA [auth BBB]	FA [auth BBB], J [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FA [auth BBB] Focus chain J [auth AAA] Interactions & Density Focus chain FA [auth BBB] Focus chain J [auth AAA]