6SCI | pdb_00006sci

Structure of AdhE form 1

• PDB DOI: https://doi.org/10.2210/pdb6SCI/pdb

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


• Deposited: 2019-07-24 Released: 2020-08-26 
• Deposition Author(s): Lovering, A.L., Bragginton, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.217 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

High-resolution structure of the alcohol dehydrogenase domain of the bifunctional bacterial enzyme AdhE.

Azmi, L., Bragginton, E.C., Cadby, I.T., Byron, O., Roe, A.J., Lovering, A.L., Gabrielsen, M.

(2020) Acta Crystallogr F Struct Biol Commun 76: 414-421

• PubMed: 32880589 
• DOI: https://doi.org/10.1107/S2053230X20010237
• Primary Citation Related Structures: 
  6SCG, 6SCI


• PubMed Abstract: 
  

  The bifunctional alcohol/aldehyde dehydrogenase (AdhE) comprises both an N-terminal aldehyde dehydrogenase (AldDH) and a C-terminal alcohol dehydrogenase (ADH). In vivo, full-length AdhE oligomerizes into long oligomers known as spirosomes. However, structural analysis of AdhE is challenging owing to the heterogeneity of the spirosomes. Therefore, the domains of AdhE are best characterized separately. Here, the structure of ADH from the pathogenic Escherichia coli O157:H7 was determined to 1.65 Å resolution. The dimeric crystal structure was confirmed in solution by small-angle X-ray scattering.

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Organizational Affiliation: 
• Institute of Infection, Immunity and Inflammation, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom.
School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.
CRUK Beatson Institute, Switchback Road, Glasgow G61 1BD, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 99.9 kDa 
• Atom Count: 6,351 
• Modeled Residue Count: 806 
• Deposited Residue Count: 910 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde-alcohol dehydrogenase	A, B	455	Escherichia coli K-12	Mutation(s): 0  Gene Names: adhE, ana, b1241, JW1228 EC: 1.1.1.1 (PDB Primary Data), 1.2.1.10 (PDB Primary Data)
UniProt
Find proteins for P0A9Q7 (Escherichia coli (strain K12)) Explore P0A9Q7  Go to UniProtKB:  P0A9Q7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A], D [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.217 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.03	α = 90
b = 96.73	β = 90
c = 122.89	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Lovering, A.L., Bragginton, E.

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 2.0: 2021-03-17
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description