6SU0

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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

  • DOI: https://doi.org/10.1039/c9cc07198a
  • Primary Citation of 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. [email protected].


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fucose-binding lectin protein89Ralstonia solanacearumMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8XXK6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QQ7 (Subject of Investigation/LOI)
Query on QQ7
Download Ideal Coordinates CCD File 
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
MFU
Query on MFU
Download Ideal Coordinates CCD File 
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
NA
Query on NA
Download Ideal Coordinates CCD File 
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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
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 LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.638α = 90
b = 94.534β = 90.06
c = 149.649γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland--

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