9BON | pdb_00009bon

Crystal structure of glucosyltransferase (GTD) domain of TpeL

PDB DOI: https://doi.org/10.2210/pdb9BON/pdb

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

Deposited: 2024-05-05 Released: 2024-08-07
Deposition Author(s): Gill, S., Sugiman-Marangos, S.N., Beilhartz, G.L., Mei, E., Taipale, M., Melnyk, R.A.
Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.237 (Depositor), 0.240 (DCC)
R-Value Work:
0.193 (Depositor), 0.190 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A diphtheria toxin-like intracellular delivery platform that evades pre-existing antidrug antibodies.

Gill, S., Sugiman-Marangos, S.N., Beilhartz, G.L., Mei, E., Taipale, M., Melnyk, R.A.

(2024) EMBO Mol Med

Macromolecule Content

Total Structure Weight: 129.58 kDa
Atom Count: 9,196
Modeled Residue Count: 1,075
Deposited Residue Count: 1,102
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TpeL	A, B	551	Clostridium perfringens	Mutation(s): 0 Gene Names: tpeL
UniProt
Find proteins for A2PYQ6 (Clostridium perfringens) Explore A2PYQ6 Go to UniProtKB: A2PYQ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2PYQ6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.237 (Depositor), 0.240 (DCC)
R-Value Work: 0.193 (Depositor), 0.190 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.093	α = 90
b = 64.73	β = 102.03
c = 121.181	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Sugiman-Marangos, S.N.

Beilhartz, G.L.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2024-08-07
Type: Initial release

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.