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), 0.239 (DCC)
R-Value Work:
0.193 (Depositor), 0.195 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.239 (DCC)
R-Value Work: 0.193 (Depositor), 0.195 (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

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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

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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.