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), 0.189 (DCC)
R-Value Work:
0.168 (Depositor)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6L8G

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

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2G285
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.189 (DCC)
R-Value Work: 0.168 (Depositor)
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

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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

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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.