6SMY

Crystal structure of SLA Reductase YihU from E. Coli with NADH and product DHPS

• PDB DOI: https://doi.org/10.2210/pdb6SMY/pdb

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


• Deposited: 2019-08-23 Released: 2020-08-12 
• Deposition Author(s): Sharma, M., Davies, G.J.
• Funding Organization(s): Leverhulme Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.270 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Literature

Dynamic Structural Changes Accompany the Production of Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase

Sharma, M., Abayakoon, P., Lingford, J.P., Epa, R., John, A., Jin, Y., Goddard-Borger, E.D., Davies, G.J., Williams, S.J.

(2020) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.9b04427

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 130 kDa 
• Atom Count: 8,004 
• Modelled Residue Count: 1,151 
• Deposited Residue Count: 1,224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-sulfolactaldehyde reductase	A, B, C, D	306	Escherichia coli K-12	Mutation(s): 0  Gene Names: yihU, b3882, JW3853 EC: 1.1.1.373
UniProt
Find proteins for P0A9V8 (Escherichia coli (strain K12)) Explore P0A9V8  Go to UniProtKB:  P0A9V8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	F [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
LLQ (Subject of Investigation/LOI)	E [auth B], G [auth C]	(2~{S})-2,3-bis(oxidanyl)propane-1-sulfonic acid C3 H8 O5 S YPFUJZAAZJXMIP-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.270 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.121	α = 90
b = 113.168	β = 90
c = 132.393	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Sharma, M., Davies, G.J.

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Funding Organization	Location	Grant Number
Leverhulme Trust	United Kingdom	RPG-2017-190

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description