6L8G | pdb_00006l8g

High resolution structure of YoeB in complex with YefM C-terminus(46N-83V) from Staphylococcus aureus.

PDB DOI: https://doi.org/10.2210/pdb6L8G/pdb

Classification: ANTITOXIN/TOXIN
Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-11-06 Released: 2020-11-11
Deposition Author(s): Yue, J., Xue, L.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free:
0.176 (Depositor), 0.180 (DCC)
R-Value Work:
0.168 (Depositor), 0.170 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structural insight into the mechanism of conditional cooperativity in the YoeB-YefM toxin-antitoxin system

Xue, L., Yue, J.

To be published.

Macromolecule Content

Total Structure Weight: 14.76 kDa
Atom Count: 1,199
Modeled Residue Count: 125
Deposited Residue Count: 126
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin	A	38	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0 Gene Names: SAOUHSC_02692
UniProt
Find proteins for Q2G285 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G285 Go to UniProtKB: Q2G285
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2G285
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YoeB	B	88	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0 Gene Names: SAOUHSC_02691
UniProt
Find proteins for Q2G286 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G286 Go to UniProtKB: Q2G286
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2G286
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.176 (Depositor), 0.180 (DCC)
R-Value Work: 0.168 (Depositor), 0.170 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.206	α = 90
b = 58.117	β = 90
c = 65.597	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-11-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	U1632124 to L.N.

Revision History (Full details and data files)

Version 1.0: 2020-11-11
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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.