7Z6F

Crystal structure of the substrate-binding protein YejA in complex with peptide fragment

• PDB DOI: https://doi.org/10.2210/pdb7Z6F/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-11 Released: 2023-09-20 
• Deposition Author(s): Beis, K., Qu, F.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.233 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Literature

Crystal structure of the substrate-binding protein YejA in complex with peptide fragment

Beis, K., Qu, F.

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: 69.45 kDa 
• Atom Count: 5,471 
• Modelled Residue Count: 593 
• Deposited Residue Count: 597 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YejA	A [auth E]	585	Escherichia coli	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
degradation peptide VAL-LEU-GLY-GLU-PRO-ARG-TYR-ALA-PHE-ASN-PHE-ASN	B [auth A]	12	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P33913 (Escherichia coli (strain K12)) Explore P33913  Go to UniProtKB:  P33913

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth E], D [auth E], E, F [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	H [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.233 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.531	α = 90
b = 76.972	β = 90
c = 103.817	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Beis, K., Qu, F.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N020103/1

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release