7ATR | pdb_00007atr

The Crystal Structure of YejA - an ABC Peptide Transporter Receptor

• PDB DOI: https://doi.org/10.2210/pdb7ATR/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-10-30 Released: 2021-11-17 
• Deposition Author(s): Ackroyd, B.K., Dodson, E.J., Wilkinson, A.J., Thomas, G.T.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.185 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.169 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of YejA - an ABC Peptide Transporter Receptor

Ackroyd, B.K., Dodson, E.J., Wilkinson, A.J., Thomas, G.H.

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: 68.73 kDa 
• Atom Count: 5,330 
• Modeled Residue Count: 591 
• Deposited Residue Count: 591 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YejA	A	580	Escherichia coli K-12	Mutation(s): 0  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
Uncharacterized protein YejA	B	11	Escherichia coli K-12	Mutation(s): 0  Gene Names: yejA, b2177, JW2165
UniProt
Find proteins for P33913 (Escherichia coli (strain K12)) Explore P33913  Go to UniProtKB:  P33913

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.185 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.169 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.44	α = 90
b = 105.267	β = 90
c = 145.387	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data processing
Aimless	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Ackroyd, B.K., Dodson, E.J., Wilkinson, A.J., Thomas, G.T.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	105501/Z/14/Z.

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description