9RT6 | pdb_00009rt6

Structure of synthetic C-terminal biotinylated schistosomin with the point mutation D88E from Biomphalaria glabrata in P21 space group

PDB DOI: https://doi.org/10.2210/pdb9RT6/pdb
Entry: 9RT6 supersedes: 9FDM

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

Deposited: 2025-07-02 Released: 2025-07-23
Deposition Author(s): Morera, S., Vigouroux, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.250 (Depositor), 0.249 (DCC)
R-Value Work:
0.207 (Depositor), 0.202 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Synthetic schistosomin from Biomphalaria glabrata

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

To be published.

Macromolecule Content

Total Structure Weight: 18.66 kDa
Atom Count: 1,402
Modeled Residue Count: 158
Deposited Residue Count: 162
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Schistosomin	A, B	81	Biomphalaria glabrata	Mutation(s): 2
UniProt
Find proteins for P24471 (Lymnaea stagnalis) Explore P24471 Go to UniProtKB: P24471
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24471
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTN Query on BTN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	D [auth A], E [auth A], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.250 (Depositor), 0.249 (DCC)
R-Value Work: 0.207 (Depositor), 0.202 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 21.764	α = 90
b = 38.411	β = 91.23
c = 87.743	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-23

Deposition Author(s):

This entry supersedes: 9FDM

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-07-23
Type: Initial release
Version 1.1: 2025-12-10
Changes: Database references, Source and taxonomy, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.