7D5N | pdb_00007d5n

Crystal structure of inositol dehydrogenase homolog complexed with NADH and myo-inositol from Azotobacter vinelandii

• PDB DOI: https://doi.org/10.2210/pdb7D5N/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Crystal structure of inositol dehydrogenase complexed with NADH and myo-inositol 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: 90.43 kDa 
• Atom Count: 6,345 
• Modeled Residue Count: 768 
• Deposited Residue Count: 802 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase	A, B	401	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	C [auth A], D [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
INS (Subject of Investigation/LOI)	E [auth B]	1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE C6 H12 O6 CDAISMWEOUEBRE-GPIVLXJGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.190 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.81	α = 90
b = 151.53	β = 90
c = 48.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	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