6DKH

The crystal structure of L-idonate 5-dehydrogenase from Escherichia coli str. K-12 substr. MG1655

• PDB DOI: https://doi.org/10.2210/pdb6DKH/pdb

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


• Deposited: 2018-05-29 Released: 2018-06-06 
• Deposition Author(s): Tan, K., Evdokimova, E., McChesney, C., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.259 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

The crystal structure of L-idonate 5-dehydrogenase from Escherichia coli str. K-12 substr. MG1655

Tan, K., Evdokimova, E., McChesney, C., Savchenko, A., Joachimiak, A.

To be published.

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 2  

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

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

Macromolecule Content

• Total Structure Weight: 150.1 kDa 
• Atom Count: 10,425 
• Modelled Residue Count: 1,382 
• Deposited Residue Count: 1,384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-idonate 5-dehydrogenase (NAD(P)(+))	A, B, C, D	346	Escherichia coli K-12	Mutation(s): 0  Gene Names: idnD, yjgV, b4267, JW4224 EC: 1.1.1.264
UniProt
Find proteins for P39346 (Escherichia coli (strain K12)) Explore P39346  Go to UniProtKB:  P39346

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.259 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.055	α = 90
b = 77.646	β = 92.62
c = 128.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-06-06 
Deposition Author(s): Tan, K., Evdokimova, E., McChesney, C., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2018-06-06
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description