6STZ | pdb_00006stz

Crystal structure of dimethylated RSLex - cucurbituril free form

PDB DOI: https://doi.org/10.2210/pdb6STZ/pdb

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

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: 1.14 Å
R-Value Free:
0.198 (Depositor), 0.193 (DCC)
R-Value Work:
0.173 (Depositor), 0.174 (DCC)
R-Value Observed:
0.174 (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: 61.25 kDa
Atom Count: 5,107
Modeled Residue Count: 529
Deposited Residue Count: 534
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	89	Ralstonia solanacearum	Mutation(s): 1 Gene Names: rsl, RUN215_v1_180133
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BDF Query on BDF Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain R [auth F] SDF format, chain Q [auth F] SDF format, chain P [auth E] SDF format, chain M [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth E] MOL2 format, chain M [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth E] mmCIF format, chain M [auth D]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F]	beta-D-fructopyranose C₆ H₁₂ O₆ LKDRXBCSQODPBY-ARQDHWQXSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F]

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	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free: 0.198 (Depositor), 0.193 (DCC)
R-Value Work: 0.173 (Depositor), 0.174 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.948	α = 90
b = 43.948	β = 90
c = 207.273	γ = 120

Software Package:

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

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	13/CDA/2168

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