5ZZU | pdb_00005zzu

Crystal structure of the C-terminal periplasmic domain of EcEptC from Escherichia coli- complex with Zn

• PDB DOI: https://doi.org/10.2210/pdb5ZZU/pdb

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


• Deposited: 2018-06-04 Released: 2019-06-05 
• Deposition Author(s): Zhao, Y.Q., Cheng, W., Gu, Y.J.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.197 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Structural and mechanistic insights into polymyxin resistance mediated by EptC originating from Escherichia coli

Zhao, Y.Q., Lai, Y.J., Zhou, D., Dou, C., Gu, Y.J., Nie, C.L., Wei, Y.Q., Cheng, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 138.21 kDa 
• Atom Count: 9,344 
• Modeled Residue Count: 1,063 
• Deposited Residue Count: 1,182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoethanolamine transferase EptC	A, B, C	394	Escherichia coli K-12	Mutation(s): 0  Gene Names: eptC, cptA, yijP, b3955, JW3927 EC: 2.7
UniProt
Find proteins for P0CB39 (Escherichia coli (strain K12)) Explore P0CB39  Go to UniProtKB:  P0CB39

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth B], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A, B, C	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.197 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.06	α = 90
b = 85.06	β = 90
c = 121.34	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SHELXS	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-05 
Deposition Author(s): Zhao, Y.Q., Cheng, W., Gu, Y.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570842

Revision History  

• Version 1.0: 2019-06-05
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary