7PR5 | pdb_00007pr5

Cocrystal of an RSL-N23H and sulfonato-thiacalix[4]arene - zinc complex

PDB DOI: https://doi.org/10.2210/pdb7PR5/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Ralstonia solanacearum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-09-20 Released: 2022-03-02
Deposition Author(s): Flood, R.J., Ramberg, K., Guagnini, F., Crowley, P.B.
Funding Organization(s): Science Foundation Ireland, Irish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.225 (Depositor), 0.223 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Protein Frameworks with Thiacalixarene and Zinc.

Flood, R.J., Ramberg, K.O., Mengel, D.B., Guagnini, F., Crowley, P.B.

(2022) Cryst Growth Des 22: 3271-3276

PubMed: 35529063 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.cgd.2c00108
Primary Citation Related Structures:
7PR2, 7PR3, 7PR4, 7PR5

PubMed Abstract:
Controlled protein assembly provides a means to generate biomaterials. Synthetic macrocycles such as the water-soluble sulfonato-calix[n]arenes are useful mediators of protein assembly. Sulfonato-thiacalix[4]arene ( tsclx ₄ ), with its metal-binding capacity, affords the potential for simultaneous macrocycle- and metal-mediated protein assembly. Here, we describe the tsclx ₄ -/Zn-directed assembly of two proteins: cationic α-helical cytochrome c (cyt c ) and neutral β-propeller Ralstonia solanacearum lectin (RSL). Two co-crystal forms were obtained with cyt c , each involving multinuclear zinc sites supported by the cone conformation of tsclx ₄ . The tsclx ₄ /Zn cluster acted as an assembly node via both lysine encapsulation and metal-mediated protein-protein contacts. In the case of RSL, tsclx ₄ adopted the 1,2-alternate conformation and supported a dinuclear zinc site with concomitant encapsulation and metal-binding of two histidine side chains. These results, together with the knowledge of thiacalixarene/metal nanoclusters, suggest promising applications for thiacalixarenes in biomaterials and MOF fabrication.

Organizational Affiliation

SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Biological and Chemical Sciences, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland.

Macromolecule Content

Total Structure Weight: 122.6 kDa
Atom Count: 9,405
Modeled Residue Count: 1,071
Deposited Residue Count: 1,080
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	90	Ralstonia solanacearum	Mutation(s): 1 Gene Names: E7Z57_08365, HXP36_18875, RSP795_21825, RSP822_19650, RUN39_v1_50103
UniProt
Find proteins for A0A0S4TLR1 (Ralstonia solanacearum) Explore A0A0S4TLR1 Go to UniProtKB: A0A0S4TLR1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0S4TLR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
80M (Subject of Investigation/LOI) Query on 80M Download:Ideal Coordinates CCD File SDF format, chain MA [auth K] MOL2 format, chain MA [auth K] mmCIF format, chain MA [auth K]	MA [auth K]	sulfonato-thiacalix[4]arene C₂₄ H₁₆ O₁₆ S₈ RUNCKYHXTXCYJH-UHFFFAOYSA-N		Interactions Focus chain MA [auth K] Interactions & Density Focus chain MA [auth K]
BDF Query on BDF Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth G] SDF format, chain CA [auth G] SDF format, chain DA [auth H] SDF format, chain JA [auth J] SDF format, chain KA [auth J] SDF format, chain N [auth A] SDF format, chain OA [auth K] SDF format, chain P [auth B] SDF format, chain QA [auth L] SDF format, chain RA [auth L] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth F] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain Q [auth B] SDF format, chain NA [auth K] SDF format, chain M [auth A] SDF format, chain HA [auth I] SDF format, chain GA [auth I] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain JA [auth J] MOL2 format, chain KA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth K] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth L] MOL2 format, chain RA [auth L] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain NA [auth K] MOL2 format, chain M [auth A] MOL2 format, chain HA [auth I] MOL2 format, chain GA [auth I] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain JA [auth J] mmCIF format, chain KA [auth J] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth K] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth L] mmCIF format, chain RA [auth L] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain NA [auth K] mmCIF format, chain M [auth A] mmCIF format, chain HA [auth I] mmCIF format, chain GA [auth I]	AA [auth F] BA [auth G] CA [auth G] DA [auth H] GA [auth I] AA [auth F], BA [auth G], CA [auth G], DA [auth H], GA [auth I], HA [auth I], JA [auth J], KA [auth J], M [auth A], N [auth A], NA [auth K], OA [auth K], P [auth B], Q [auth B], QA [auth L], RA [auth L], S [auth C], T [auth C], U [auth D], V [auth D], X [auth E], Y [auth E], Z [auth F]	beta-D-fructopyranose C₆ H₁₂ O₆ LKDRXBCSQODPBY-ARQDHWQXSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain KA [auth J] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth K] Focus chain OA [auth K] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth L] Focus chain RA [auth L] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain KA [auth J] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth K] Focus chain OA [auth K] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth L] Focus chain RA [auth L] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth H] MOL2 format, chain EA [auth H] mmCIF format, chain EA [auth H]	EA [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth H] Interactions & Density Focus chain EA [auth H]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain PA [auth K] SDF format, chain R [auth B] SDF format, chain W [auth D] SDF format, chain O [auth A] SDF format, chain LA [auth J] SDF format, chain IA [auth I] SDF format, chain FA [auth H] MOL2 format, chain PA [auth K] MOL2 format, chain R [auth B] MOL2 format, chain W [auth D] MOL2 format, chain O [auth A] MOL2 format, chain LA [auth J] MOL2 format, chain IA [auth I] MOL2 format, chain FA [auth H] mmCIF format, chain PA [auth K] mmCIF format, chain R [auth B] mmCIF format, chain W [auth D] mmCIF format, chain O [auth A] mmCIF format, chain LA [auth J] mmCIF format, chain IA [auth I] mmCIF format, chain FA [auth H]	FA [auth H] IA [auth I] LA [auth J] O [auth A] PA [auth K] FA [auth H], IA [auth I], LA [auth J], O [auth A], PA [auth K], R [auth B], W [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain FA [auth H] Focus chain IA [auth I] Focus chain LA [auth J] Focus chain O [auth A] Focus chain PA [auth K] Focus chain R [auth B] Focus chain W [auth D] Interactions & Density Focus chain FA [auth H] Focus chain IA [auth I] Focus chain LA [auth J] Focus chain O [auth A] Focus chain PA [auth K] Focus chain R [auth B] Focus chain W [auth D]