7D5M

Crystal structure of inositol dehydrogenase homolog complexed with NAD+ from Azotobacter vinelandii

• PDB DOI: https://doi.org/10.2210/pdb7D5M/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Azotobacter vinelandii DJ
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-09-27 Released: 2021-09-29 
• Deposition Author(s): Fukano, K., Ono, T., Suzuki, M., Takenoya, M., Ito, S., Sasaki, Y., Yajima, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.193 
• R-Value Work: 0.179 

Starting Model: experimental

Literature

Crystal structure of inositol dehydrogenase complexed with NAD+ from Azotobacter vinelandii

Fukano, K., Ono, T., Suzuki, M., Takenoya, M., Ito, S., Sasaki, Y., Yajima, S.

To be published.

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: homology

Macromolecule Content

• Total Structure Weight: 44.8 kDa 
• Atom Count: 3,344 
• Modelled Residue Count: 389 
• Deposited Residue Count: 397 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase	A	397	Azotobacter vinelandii DJ	Mutation(s): 0  Gene Names: Avin_50260
UniProt
Find proteins for C1DLC3 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DLC3  Go to UniProtKB:  C1DLC3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.193 
• R-Value Work: 0.179 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.25	α = 90
b = 107.997	β = 90
c = 156.759	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-29 
Deposition Author(s): Fukano, K., Ono, T., Suzuki, M., Takenoya, M., Ito, S., Sasaki, Y., Yajima, S.

Revision History  

• Version 1.0: 2021-09-29
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Derived calculations, Refinement description