4N54 | pdb_00004n54

Crystal structure of scyllo-inositol dehydrogenase from Lactobacillus casei with bound cofactor NAD(H) and scyllo-inositol

• PDB DOI: https://doi.org/10.2210/pdb4N54/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lacticaseibacillus casei BL23
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-09 Released: 2015-04-15 
• Deposition Author(s): Bertwistle, D., Sanders, D.A.R., Palmer, D.R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.261 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of scyllo-inositol dehydrogenase from Lactobacillus casei with bound cofactor NAD(H) and scyllo-inositol

Bertwistle, D., Aamudalapalli, H., Sanders, D.A.R., Palmer, D.R.J.

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)

Macromolecule Content 

• Total Structure Weight: 158.08 kDa 
• Atom Count: 10,913 
• Modeled Residue Count: 1,360 
• Deposited Residue Count: 1,408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol dehydrogenase	A, B, C, D	352	Lacticaseibacillus casei BL23	Mutation(s): 0  Gene Names: idh, iolG, iolG2, LCABL_02220 EC: 1.1.1
UniProt
Find proteins for A0A0J9X1Y7 (Lacticaseibacillus casei (strain BL23)) Explore A0A0J9X1Y7  Go to UniProtKB:  A0A0J9X1Y7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	E [auth A], G [auth B], I [auth C], J [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
2H3	F [auth A], H [auth B], K [auth D]	(1r,2r,3r,4r,5r,6r)-cyclohexane-1,2,3,4,5,6-hexol C6 H12 O6 CDAISMWEOUEBRE-CDRYSYESSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.261 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.25	α = 90
b = 99.83	β = 90
c = 192.51	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxDC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-15 
Deposition Author(s): Bertwistle, D., Sanders, D.A.R., Palmer, D.R.J.

Revision History  

• Version 1.0: 2015-04-15
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description