2GA4 | pdb_00002ga4

Stx2 with adenine

PDB DOI: https://doi.org/10.2210/pdb2GA4/pdb

Classification: TOXIN
Organism(s): Escherichia phage 933W
Mutation(s): No

Deposited: 2006-03-07 Released: 2006-07-11
Deposition Author(s): Fraser, M.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.183 (Depositor), 0.180 (DCC)
R-Value Work:
0.156 (Depositor), 0.153 (DCC)
R-Value Observed:
0.157 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Binding of adenine to Stx2, the protein toxin from Escherichia coli O157:H7.

Fraser, M.E., Cherney, M.M., Marcato, P., Mulvey, G.L., Armstrong, G.D., James, M.N.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 627-630

PubMed: 16820678 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309106021968
Primary Citation Related Structures:
2GA4

PubMed Abstract:
Stx2 is a protein toxin whose catalytic subunit acts as an N-glycosidase to depurinate a specific adenine base from 28S rRNA. In the holotoxin, the catalytic portion, A1, is linked to the rest of the A subunit, A2, and A2 interacts with the pentameric ring formed by the five B subunits. In order to test whether the holotoxin is active as an N-glycosidase, Stx2 was crystallized in the presence of adenosine and adenine. The crystals diffracted to approximately 1.8 angstroms and showed clear electron density for adenine in the active site. Adenosine had been cleaved, proving that Stx2 is an active N-glycosidase. While the holotoxin is active against small substrates, it would be expected that the B subunits would interfere with the binding of the 28S rRNA.

Organizational Affiliation

Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary AB T2N 1N4, Canada. frasm@ucalgary.ca

Macromolecule Content

Total Structure Weight: 73.7 kDa
Atom Count: 5,605
Modeled Residue Count: 633
Deposited Residue Count: 647
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shiga-like toxin II subunit A	A	297	Escherichia phage 933W	Mutation(s): 0 EC: 3.2.2.22
UniProt
Find proteins for P09385 (Escherichia phage 933W) Explore P09385 Go to UniProtKB: P09385
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09385
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Shiga-like toxin II subunit B	B, C, D, E, F	70	Escherichia phage 933W	Mutation(s): 0
UniProt
Find proteins for P09386 (Escherichia phage 933W) Explore P09386 Go to UniProtKB: P09386
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09386
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PS Query on 1PS Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain U [auth F] SDF format, chain Q [auth D] SDF format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain U [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain U [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth B]	N [auth B], O [auth C], Q [auth D], U [auth F]	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE C₈ H₁₁ N O₃ S REEBJQTUIJTGAL-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain U [auth F] Interactions & Density Focus chain N [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain U [auth F]
ADE Query on ADE Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth F] MOL2 format, chain V [auth F] mmCIF format, chain V [auth F]	V [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain V [auth F] Interactions & Density Focus chain V [auth F]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain R [auth D] SDF format, chain P [auth C] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain S [auth E] MOL2 format, chain R [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain S [auth E] mmCIF format, chain R [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], P [auth C], R [auth D], S [auth E]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth E] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth E]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain T [auth F] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain T [auth F] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], M [auth B], T [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain T [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.183 (Depositor), 0.180 (DCC)
R-Value Work: 0.156 (Depositor), 0.153 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.55	α = 90
b = 144.55	β = 90
c = 59.42	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
XFIT	data reduction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-07-11

Deposition Author(s):

Fraser, M.E.

Revision History (Full details and data files)

Version 1.0: 2006-07-11
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary