8FSS

Complex Structure of YejA-S481A with Microcin C7

• PDB DOI: https://doi.org/10.2210/pdb8FSS/pdb

• Classification: PEPTIDE BINDING PROTEIN/ANTIBIOTIC
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-01-11 Released: 2024-02-07 
• Deposition Author(s): Naik, S.K., Dong, S.-H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.219 
• R-Value Observed: 0.219 

Literature

Trojan Horse Peptide Conjugates Remodel the Activity Spectrum of Clinical Antibiotics

Luo, S., Dong, S.-H., Nair, S.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.52 kDa 
• Atom Count: 5,275 
• Modelled Residue Count: 578 
• Deposited Residue Count: 593 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YejA	A	586	Escherichia coli	Mutation(s): 1  Gene Names: yejA, b2177, JW2165
UniProt
Find proteins for P33913 (Escherichia coli (strain K12)) Explore P33913  Go to UniProtKB:  P33913

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Microcin C7 peptide portion	B	7	Escherichia coli	Mutation(s): 1
UniProt
Find proteins for Q47505 (Escherichia coli) Explore Q47505  Go to UniProtKB:  Q47505

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7MO (Subject of Investigation/LOI)	C [auth B]	5'-O-[(R)-amino(3-aminopropoxy)phosphoryl]adenosine C13 H22 N7 O6 P MBMBAANIBYMPLC-LGVJOIAUSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
FME	B	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.219 
• R-Value Observed: 0.219 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.089	α = 90
b = 102.834	β = 90
c = 144.381	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
autoPROC	data processing
XDS	data scaling
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Naik, S.K., Dong, S.-H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM131347
National Natural Science Foundation of China (NSFC)	China	21907046

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release