6SU0 | pdb_00006su0

Crystal structure of dimethylated RSLex in complex with cucurbit[7]uril

PDB DOI: https://doi.org/10.2210/pdb6SU0/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Ralstonia solanacearum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-09-12 Released: 2020-02-19
Deposition Author(s): Guagnini, F., Engilberge, S., Crowley, P.B.
Funding Organization(s): Science Foundation Ireland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.311 (Depositor), 0.297 (DCC)
R-Value Work:
0.247 (Depositor), 0.238 (DCC)
R-Value Observed:
0.250 (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

Engineered assembly of a protein-cucurbituril biohybrid.

Guagnini, F., Engilberge, S., Ramberg, K.O., Perez, J., Crowley, P.B.

(2020) Chem Commun (Camb) 56: 360-363

PubMed: 31825399 Search on PubMed
DOI: https://doi.org/10.1039/c9cc07198a
Primary Citation Related Structures:
6STZ, 6SU0

PubMed Abstract:
A crystalline biohybrid with a 4 : 1 protein : cucurbituril mass ratio is presented. This result was achieved by engineering additional cucurbit[7]uril (Q7) binding sites into a β-propeller protein. In contrast to the parent protein, Q7-controlled assembly of the engineered variant occurred in solution, as evidenced by NMR and SAXS measurements.

Organizational Affiliation

School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland. peter.crowley@nuigalway.ie.

Macromolecule Content

Total Structure Weight: 134.41 kDa
Atom Count: 9,770
Modeled Residue Count: 1,068
Deposited Residue Count: 1,068
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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 [auth I], H [auth J], I [auth K], J [auth M], K [auth N], L [auth O]	89	Ralstonia solanacearum	Mutation(s): 0 Gene Names: RSP795_21825, RSP799_05830, RSP822_19650, RUN39_v1_50103
UniProt
Find proteins for Q8XXK6 (Ralstonia nicotianae (strain ATCC BAA-1114 / GMI1000)) Explore Q8XXK6 Go to UniProtKB: Q8XXK6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8XXK6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QQ7 (Subject of Investigation/LOI) Query on QQ7 Download:Ideal Coordinates CCD File SDF format, chain DA [auth I] SDF format, chain FA [auth J] SDF format, chain GA [auth K] SDF format, chain HA [auth M] SDF format, chain IA [auth M] SDF format, chain JA [auth N] SDF format, chain KA [auth N] SDF format, chain MA [auth O] SDF format, chain N [auth A] SDF format, chain NA [auth O] SDF format, chain Q [auth B] SDF format, chain V [auth C] MOL2 format, chain DA [auth I] MOL2 format, chain FA [auth J] MOL2 format, chain GA [auth K] MOL2 format, chain HA [auth M] MOL2 format, chain IA [auth M] MOL2 format, chain JA [auth N] MOL2 format, chain KA [auth N] MOL2 format, chain MA [auth O] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth O] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] mmCIF format, chain DA [auth I] mmCIF format, chain FA [auth J] mmCIF format, chain GA [auth K] mmCIF format, chain HA [auth M] mmCIF format, chain IA [auth M] mmCIF format, chain JA [auth N] mmCIF format, chain KA [auth N] mmCIF format, chain MA [auth O] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth O] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C]	DA [auth I] FA [auth J] GA [auth K] HA [auth M] IA [auth M] DA [auth I], FA [auth J], GA [auth K], HA [auth M], IA [auth M], JA [auth N], KA [auth N], MA [auth O], N [auth A], NA [auth O], Q [auth B], V [auth C]	cucurbit[7]uril C₄₂ H₄₂ N₂₈ O₁₄ ZDOBFUIMGBWEAB-XGFHMVPTSA-N		Interactions Focus chain DA [auth I] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain HA [auth M] Focus chain IA [auth M] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain MA [auth O] Focus chain N [auth A] Focus chain NA [auth O] Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain DA [auth I] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain HA [auth M] Focus chain IA [auth M] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain MA [auth O] Focus chain N [auth A] Focus chain NA [auth O] Focus chain Q [auth B] Focus chain V [auth C]
MFU Query on MFU Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth F] SDF format, chain EA [auth I] SDF format, chain LA [auth N] SDF format, chain P [auth A] SDF format, chain PA [auth O] SDF format, chain R [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth D] SDF format, chain OA [auth O] SDF format, chain O [auth A] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain EA [auth I] MOL2 format, chain LA [auth N] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth O] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain OA [auth O] MOL2 format, chain O [auth A] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain EA [auth I] mmCIF format, chain LA [auth N] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth O] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain OA [auth O] mmCIF format, chain O [auth A]	AA [auth E] CA [auth F] EA [auth I] LA [auth N] O [auth A] AA [auth E], CA [auth F], EA [auth I], LA [auth N], O [auth A], OA [auth O], P [auth A], PA [auth O], R [auth B], W [auth C], X [auth C], Z [auth D]	methyl alpha-L-fucopyranoside C₇ H₁₄ O₅ OHWCAVRRXKJCRB-CXNFULCWSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain EA [auth I] Focus chain LA [auth N] Focus chain O [auth A] Focus chain OA [auth O] Focus chain P [auth A] Focus chain PA [auth O] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain EA [auth I] Focus chain LA [auth N] Focus chain O [auth A] Focus chain OA [auth O] Focus chain P [auth A] Focus chain PA [auth O] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain M [auth A] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain Y [auth D] SDF format, chain S [auth C] MOL2 format, chain BA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain S [auth C] mmCIF format, chain BA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain S [auth C]	BA [auth F] M [auth A] S [auth C] T [auth C] U [auth C] BA [auth F], M [auth A], S [auth C], T [auth C], U [auth C], Y [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain M [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth F] Focus chain M [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A B C D E A, B, C, D, E, F, G [auth I], H [auth J], I [auth K], J [auth M], K [auth N], L [auth O]	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.311 (Depositor), 0.297 (DCC)
R-Value Work: 0.247 (Depositor), 0.238 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.638	α = 90
b = 94.534	β = 90.06
c = 149.649	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-02-19

Deposition Author(s):

Guagnini, F.

Engilberge, S.

Crowley, P.B.

Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	--

Revision History (Full details and data files)

Version 1.0: 2020-02-19
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary