6UL4 | pdb_00006ul4

Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLO-G11

PDB DOI: https://doi.org/10.2210/pdb6UL4/pdb

Classification: TOXIN/ANTITOXIN
Organism(s): Clostridium botulinum, Vicugna pacos
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-10-06 Released: 2020-03-04
Deposition Author(s): Lam, K., Jin, R.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free:
0.258 (Depositor), 0.261 (DCC)
R-Value Work:
0.204 (Depositor), 0.206 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Structural Insights into Rational Design of Single-Domain Antibody-Based Antitoxins against Botulinum Neurotoxins

Lam, K., Tremblay, J.M., Vazquez-Cintron, E., Perry, K., Ondeck, C., Webb, R., McNutt, P.M., Shoemaker, C.B., Jin, R.

(2020) Cell Rep 30: 2526

DOI: https://doi.org/10.1016/j.celrep.2020.01.107

Macromolecule Content

Total Structure Weight: 69.37 kDa
Atom Count: 4,599
Modeled Residue Count: 553
Deposited Residue Count: 593
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Botulinum neurotoxin type B	A	438	Clostridium botulinum	Mutation(s): 0 Gene Names: botB EC: 3.4.24.69
UniProt
Find proteins for P10844 (Clostridium botulinum) Explore P10844 Go to UniProtKB: P10844
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10844
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH JLO-G11	B	155	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free: 0.258 (Depositor), 0.261 (DCC)
R-Value Work: 0.204 (Depositor), 0.206 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.299	α = 90
b = 267.905	β = 90
c = 144.693	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
Coot	model building
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-03-04
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: 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.