7BWF | pdb_00007bwf

YoeB-YefM complex from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb7BWF/pdb

• Classification: TOXIN/ANTITOXIN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-14 Released: 2020-05-20 
• Deposition Author(s): Lee, B.-J., Eun, H.-J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the YoeBSa1-YefMSa1 complex from Staphylococcus aureus.

Eun, H.-J., Lee, K.-Y., Kim, D.-G., Im, D.S., Lee, B.-J.

(2020) Biochem Biophys Res Commun 527: 264-269

• DOI: https://doi.org/10.1016/j.bbrc.2020.04.089

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.24 kDa 
• Atom Count: 3,060 
• Modeled Residue Count: 357 
• Deposited Residue Count: 357 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Addiction module antitoxin RelB	A, C	87	Staphylococcus aureus	Mutation(s): 0  Gene Names: M1K003_0948, SAKG03_24000
UniProt
Find proteins for A0A3A3ATA4 (Staphylococcus aureus) Explore A0A3A3ATA4  Go to UniProtKB:  A0A3A3ATA4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin	B	92	Staphylococcus aureus	Mutation(s): 0  Gene Names:  yefM, BTN44_14530, EP54_09735, EQ90_00255, HMPREF3211_00052, M1K003_0949, NCTC10654_02579, NCTC10702_03766, NCTC5664_01444, NCTC6133_03236, NCTC7988_02488, RK64_12840, SAKG03_24010
UniProt
Find proteins for A0A0B4ND47 (Staphylococcus aureus) Explore A0A0B4ND47  Go to UniProtKB:  A0A0B4ND47

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin	D	91	Staphylococcus aureus	Mutation(s): 0  Gene Names:  yefM, BTN44_14530, EP54_09735, EQ90_00255, HMPREF3211_00052, M1K003_0949, NCTC10654_02579, NCTC10702_03766, NCTC5664_01444, NCTC6133_03236, NCTC7988_02488, RK64_12840, SAKG03_24010
UniProt
Find proteins for A0A0B4ND47 (Staphylococcus aureus) Explore A0A0B4ND47  Go to UniProtKB:  A0A0B4ND47

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.849	α = 90
b = 67.849	β = 90
c = 69.356	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Lee, B.-J., Eun, H.-J.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2018R1A2A1A19018526
National Research Foundation (NRF, Korea)	Korea, Republic Of	2018R1A5A2024425
National Research Foundation (NRF, Korea)	Korea, Republic Of	2019 BK21 Plus Project for Medicine, Dentistry and Pharmacy

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description