6UL6

Crystal Structure of BoNT/A-LCHn domain in complex with VNA ciA-D12/11/ciA-B5 and VHH ciA-H7

PDB DOI: https://doi.org/10.2210/pdb6UL6/pdb

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

Deposited: 2019-10-07 Released: 2020-03-04
Deposition Author(s): Lam, K., Jin, R.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.194
R-Value Work: 0.183
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

Currently 6UL6 does not have a validation slider image.

This is version 1.1 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: 141.99 kDa
Atom Count: 10,407
Modelled Residue Count: 1,208
Deposited Residue Count: 1,261
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BoNT/A	A	873	Clostridium botulinum	Mutation(s): 0 Gene Names: a, A, boNT, bonta, ACP52_06670 EC: 3.4.24.69
UniProt
Find proteins for P0DPI1 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)) Explore P0DPI1 Go to UniProtKB: P0DPI1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DPI1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ciA-D12/11/ciA-B5	B	265	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ciA-H7	C	123	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.194
R-Value Work: 0.183
R-Value Observed: 0.183
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.288	α = 90
b = 90.253	β = 119.037
c = 144.771	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Currently 6UL6 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

Released Date: 2020-03-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.