6G8U

Crystal structure of the light chain of botulinum neurotoxin X (residues 2-427)

PDB DOI: https://doi.org/10.2210/pdb6G8U/pdb

Classification: TOXIN
Organism(s): Clostridium botulinum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-04-10 Released: 2019-07-31
Deposition Author(s): Wu, Y., Kammerer, R.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free: 0.169
R-Value Work: 0.149
R-Value Observed: 0.150

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the light chain of botulinum neurotoxin X (residues 2-427)

Wu, Y., Kammerer, R.

To be published.

Macromolecule Content

Total Structure Weight: 50.4 kDa
Atom Count: 3,874
Modelled Residue Count: 413
Deposited Residue Count: 443
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of botulinum neurotoxin X (res. 2-427)	A	443	Clostridium botulinum	Mutation(s): 0
UniProt
Find proteins for P0DPK1 (Clostridium botulinum) Explore P0DPK1 Go to UniProtKB: P0DPK1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DPK1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free: 0.169
R-Value Work: 0.149
R-Value Observed: 0.150
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.6	α = 90
b = 86.95	β = 90
c = 93.39	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-07-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A_163449

Revision History (Full details and data files)

Version 1.0: 2019-07-31
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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 R01GM133198.