9FDO | pdb_00009fdo

Structure of synthetic C-terminal biotinylated schistosomin with the point mutation D88E from Biomphalaria glabrata in C2 space group

• PDB DOI: https://doi.org/10.2210/pdb9FDO/pdb

• Classification: TOXIN
• Organism(s): Biomphalaria glabrata
• Mutation(s): Yes 


• Deposited: 2024-05-17 Released: 2025-05-28 
• Deposition Author(s): Morera, S., Vigouroux, A., Legrand, P.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.275 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Synthetic schistosomin from Biomphalaria glabrata

Morera, S., Vigouroux, A., Legrand, P., Vicogne, J., Melnyk, O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.66 kDa 
• Atom Count: 1,348 
• Modeled Residue Count: 158 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Schistosomin	A, B	80	Biomphalaria glabrata	Mutation(s): 1
UniProt
Find proteins for B5L013 (Biomphalaria glabrata) Explore B5L013  Go to UniProtKB:  B5L013

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTN	C [auth A], E [auth B]	BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-ZKWXMUAHSA-N
SO4	D [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.275 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.68	α = 90
b = 37.96	β = 95.35
c = 43.19	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
autoPROC	data processing
autoPROC	data processing
XSCALE	data scaling
BUSTER	refinement
autoPROC	data reduction
PHASER	phasing
STARANISO	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Morera, S., Vigouroux, A., Legrand, P.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Data collection, Database references, Refinement description, Source and taxonomy, Structure summary