7E7R | pdb_00007e7r

Crystal structure of RSL mutant in complex with Ligand

• PDB DOI: https://doi.org/10.2210/pdb7E7R/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Ralstonia solanacearum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-02-27 Released: 2021-04-14 
• Deposition Author(s): Li, L., Chen, G.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.285 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Starting Model: experimental

Literature

Spatiotemporal Landscape for the Sophisticated Transformation of Protein Assemblies Defined by Multiple Supramolecular Interactions.

Li, L., Li, Z., Wang, Z., Chen, S., Liu, R., Xu, X., Zhang, Z., Ye, L., Ding, Y., Luo, Q., Cao, S., Zhang, L., Imberty, A., Chen, G.

(2023) ACS Nano 17: 15001-15011

• PubMed: 37459282 
• DOI: https://doi.org/10.1021/acsnano.3c04029
• Primary Citation Related Structures: 
  7E7N, 7E7R, 7E7T, 7E7U, 7E7V, 7E7W


• PubMed Abstract: 
  

  Precise protein assemblies not only constitute a series of living machineries but also provide an advanced class of biomaterials. Previously, we developed the inducing ligand strategy to generate various fixed protein assemblies, without the formation of noncovalent interactions between proteins. Here, we demonstrated that controlling the symmetry and number of supramolecular interactions introduced on protein surfaces could direct the formation of unspecific interactions between proteins and induce various nanoscale assemblies, including coiling nanowires, nanotubes, and nanosheets, without manipulation of the protein's native surfaces. More importantly, these nanoscale assemblies could spontaneously evolve into more ordered architectures, crystals. We further showed that the transformation from the introduced supramolecular interactions to the interactions formed between proteins was crucial for pathway selection and outcomes of evolution. These findings reveal a transformation mechanism of protein self-assembly that has not been exploited before and may provide an approach to generate complex and transformable biomacromolecular self-assemblies.

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Organizational Affiliation: 
• The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.
MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049, China.
State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and Trauma, Hainan Medical University, Haikou 571199, China.
CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.
Université Grenoble Alpes, CNRS, CERMAV, Grenoble 38000, France.
Multiscale Research Institute for Complex Systems, Fudan University, Shanghai 200433, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.74 kDa 
• Atom Count: 4,641 
• Modeled Residue Count: 514 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein	A, B	272	Ralstonia solanacearum	Mutation(s): 3  Gene Names: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
UniProt
Find proteins for A0A0S4WQH1 (Ralstonia solanacearum) Explore A0A0S4WQH1  Go to UniProtKB:  A0A0S4WQH1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R2F (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	2-[2-[4-[[(2R,3S,4R,5S,6S)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-1,2,3-triazol-1-yl]ethoxy]ethyl 2-[3,6-bis(diethylamino)-9H-xanthen-9-yl]benzoate C41 H53 N5 O9 ODXMNHGJTHCYBO-XFBFBVLGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.285 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.427	α = 90
b = 81.959	β = 90
c = 97.116	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
autoPROC	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-14 
Deposition Author(s): Li, L., Chen, G.S.

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2026-07-29
  Changes: Database references, Structure summary