7AB3 | pdb_00007ab3

Crystal structure of the Escherichia coli toxin-antitoxin system HipBST (HipT S57A)

PDB DOI: https://doi.org/10.2210/pdb7AB3/pdb

Classification: TOXIN
Organism(s): Escherichia coli O127:H6 str. E2348/69
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-09-06 Released: 2022-01-12
Deposition Author(s): Baerentsen, R.L., Brodersen, D.E.
Funding Organization(s): Novo Nordisk Foundation, Danish National Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.236 (Depositor), 0.246 (DCC)
R-Value Work:
0.199 (Depositor), 0.211 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural basis for regulation of a tripartite toxin-antitoxin system by dual phosphorylation

Baerentsen, R.L., Nielsen, S.V., Lyngso, J., Bisiak, F., Pedersen, J.S., Gerdes, K., Sorensen, M.A., Brodersen, D.E.

(2022) bioRxiv

DOI: https://doi.org/10.1101/2022.01.28.478185

Macromolecule Content

Total Structure Weight: 125.92 kDa
Atom Count: 8,668
Modeled Residue Count: 1,015
Deposited Residue Count: 1,102
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted transcriptional regulator, XRE family	A, D	107	Escherichia coli O127:H6 str. E2348/69	Mutation(s): 0 Gene Names: E2348C_3787
UniProt
Find proteins for B7UL98 (Escherichia coli O127:H6 (strain E2348/69 / EPEC)) Explore B7UL98 Go to UniProtKB: B7UL98
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7UL98
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Couple_hipA domain-containing protein	B, E	103	Escherichia coli O127:H6 str. E2348/69	Mutation(s): 0 Gene Names: E2348C_3786
UniProt
Find proteins for B7UL97 (Escherichia coli O127:H6 (strain E2348/69 / EPEC)) Explore B7UL97 Go to UniProtKB: B7UL97
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7UL97
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HipA_C domain-containing protein	C, F	341	Escherichia coli O127:H6 str. E2348/69	Mutation(s): 1 Gene Names: E2348C_3785
UniProt
Find proteins for B7UL96 (Escherichia coli O127:H6 (strain E2348/69 / EPEC)) Explore B7UL96 Go to UniProtKB: B7UL96
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7UL96
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	C, F	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.236 (Depositor), 0.246 (DCC)
R-Value Work: 0.199 (Depositor), 0.211 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 281.68	α = 90
b = 106.07	β = 90.648
c = 57.56	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-12

Deposition Author(s):

Baerentsen, R.L.

Brodersen, D.E.

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF18OC0030646
Danish National Research Foundation	Denmark	DNRF120

Revision History (Full details and data files)

Version 1.0: 2022-01-12
Type: Initial release
Version 1.1: 2022-08-03
Changes: Database references
Version 1.2: 2024-01-31
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary