8OXS | pdb_00008oxs

Cholera holotoxin variant (chimera with E. coli heat-labile enterotoxin, 4 C-terminal substitutions)

PDB DOI: https://doi.org/10.2210/pdb8OXS/pdb

Classification: TOXIN
Organism(s): Vibrio cholerae O1
Expression System: Vibrio natriegens
Mutation(s): Yes

Deposited: 2023-05-02 Released: 2024-08-14
Deposition Author(s): Kersten, F., Heim, J.B., Cordara, G., Krengel, U.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.224 (Depositor), 0.230 (DCC)
R-Value Work:
0.193 (Depositor), 0.200 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Cholera toxin variants

Heim, J.B., Serrano, A., Kersten, F., Mojica, N., Cordara, G., Tatulian, S.A., Krengel, U., Teter, K.

To be published.

Macromolecule Content

Total Structure Weight: 174.83 kDa
Atom Count: 13,700
Modeled Residue Count: 1,492
Deposited Residue Count: 1,510
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholera enterotoxin subunit A	A, G [auth B]	240	Vibrio cholerae O1	Mutation(s): 4 Gene Names: ctxA, toxA, VC_1457
UniProt
Find proteins for P01555 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore P01555 Go to UniProtKB: P01555
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01555
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholera enterotoxin subunit B	B [auth D] C [auth E] D [auth F] E [auth G] F [auth H] B [auth D], C [auth E], D [auth F], E [auth G], F [auth H], H [auth C], I, J, K, L	103	Vibrio cholerae O1	Mutation(s): 2 Gene Names: ctxB, toxB, VC_1456
UniProt
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore P01556 Go to UniProtKB: P01556
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01556
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain DA [auth I] SDF format, chain Q [auth E] SDF format, chain W [auth H] MOL2 format, chain AA [auth B] MOL2 format, chain DA [auth I] MOL2 format, chain Q [auth E] MOL2 format, chain W [auth H] mmCIF format, chain AA [auth B] mmCIF format, chain DA [auth I] mmCIF format, chain Q [auth E] mmCIF format, chain W [auth H]	AA [auth B], DA [auth I], Q [auth E], W [auth H]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain DA [auth I] Focus chain Q [auth E] Focus chain W [auth H] Interactions & Density Focus chain AA [auth B] Focus chain DA [auth I] Focus chain Q [auth E] Focus chain W [auth H]
GLA Query on GLA Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain FA [auth K] SDF format, chain HA [auth L] SDF format, chain O [auth D] SDF format, chain R [auth E] SDF format, chain V [auth G] SDF format, chain Y [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain FA [auth K] MOL2 format, chain HA [auth L] MOL2 format, chain O [auth D] MOL2 format, chain R [auth E] MOL2 format, chain V [auth G] MOL2 format, chain Y [auth H] mmCIF format, chain BA [auth C] mmCIF format, chain FA [auth K] mmCIF format, chain HA [auth L] mmCIF format, chain O [auth D] mmCIF format, chain R [auth E] mmCIF format, chain V [auth G] mmCIF format, chain Y [auth H]	BA [auth C] FA [auth K] HA [auth L] O [auth D] R [auth E] BA [auth C], FA [auth K], HA [auth L], O [auth D], R [auth E], V [auth G], Y [auth H]	alpha-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PHYPRBDBSA-N		Interactions Focus chain BA [auth C] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain O [auth D] Focus chain R [auth E] Focus chain V [auth G] Focus chain Y [auth H] Interactions & Density Focus chain BA [auth C] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain O [auth D] Focus chain R [auth E] Focus chain V [auth G] Focus chain Y [auth H]
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain EA [auth I] SDF format, chain GA [auth K] SDF format, chain N [auth A] SDF format, chain P [auth D] SDF format, chain T [auth F] SDF format, chain U [auth G] SDF format, chain X [auth H] SDF format, chain S [auth E] SDF format, chain IA [auth L] MOL2 format, chain CA [auth C] MOL2 format, chain EA [auth I] MOL2 format, chain GA [auth K] MOL2 format, chain N [auth A] MOL2 format, chain P [auth D] MOL2 format, chain T [auth F] MOL2 format, chain U [auth G] MOL2 format, chain X [auth H] MOL2 format, chain S [auth E] MOL2 format, chain IA [auth L] mmCIF format, chain CA [auth C] mmCIF format, chain EA [auth I] mmCIF format, chain GA [auth K] mmCIF format, chain N [auth A] mmCIF format, chain P [auth D] mmCIF format, chain T [auth F] mmCIF format, chain U [auth G] mmCIF format, chain X [auth H] mmCIF format, chain S [auth E] mmCIF format, chain IA [auth L]	CA [auth C] EA [auth I] GA [auth K] IA [auth L] N [auth A] CA [auth C], EA [auth I], GA [auth K], IA [auth L], N [auth A], P [auth D], S [auth E], T [auth F], U [auth G], X [auth H]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain CA [auth C] Focus chain EA [auth I] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain N [auth A] Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain X [auth H] Interactions & Density Focus chain CA [auth C] Focus chain EA [auth I] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain N [auth A] Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain X [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain M [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain M [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain M [auth A]	M [auth A], Z [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain Z [auth B] Interactions & Density Focus chain M [auth A] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.224 (Depositor), 0.230 (DCC)
R-Value Work: 0.193 (Depositor), 0.200 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.295	α = 90
b = 89.61	β = 98.186
c = 141.094	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building
MxCuBE	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R03AI112854
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI137056