6G8U | pdb_00006g8u

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 (Depositor), 0.171 (DCC)
R-Value Work:
0.149 (Depositor), 0.152 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 413
Deposited Residue Count: 443
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.171 (DCC)
R-Value Work: 0.149 (Depositor), 0.152 (DCC)
R-Value Observed: 0.150 (Depositor)

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

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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

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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.