8IVJ | pdb_00008ivj

Candida boidinii Formate Dehydrogenase V120T Mutant

• PDB DOI: https://doi.org/10.2210/pdb8IVJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): [Candida] boidinii
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2023-03-28 Released: 2023-05-10 
• Deposition Author(s): Gul, M., Yuksel, B., Bulut, H., DeMirci, H.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: in silico

Literature

Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography.

Gul, M., Yuksel, B., Bulut, H., DeMirci, H.

(2023) Acta Crystallogr D Struct Biol 79: 1010-1017

• PubMed: 37860962 
• DOI: https://doi.org/10.1107/S2059798323008070
• Primary Citation Related Structures: 
  8HTY, 8IQ7, 8IVJ


• PubMed Abstract: 
  

  Candida boidinii NAD ⁺ -dependent formate dehydrogenase (CbFDH) has gained significant attention for its potential application in the production of biofuels and various industrial chemicals from inorganic carbon dioxide. The present study reports the atomic X-ray crystal structures of wild-type CbFDH at cryogenic and ambient temperatures, as well as that of the Val120Thr mutant at cryogenic temperature, determined at the Turkish Light Source `Turkish DeLight'. The structures reveal new hydrogen bonds between Thr120 and water molecules in the active site of the mutant CbFDH, suggesting increased stability of the active site and more efficient electron transfer during the reaction. Further experimental data is needed to test these hypotheses. Collectively, these findings provide invaluable insights into future protein-engineering efforts that could potentially enhance the efficiency and effectiveness of CbFDH.

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Organizational Affiliation: 
• Department of Molecular Biology and Genetics, Koc University, 34450 Istanbul, Türkiye.
Department of Medical Biochemistry, Faculty of Medicine, Istinye University, 34010 Istanbul, Türkiye.

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 Evidence: native gel electrophoresis

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: 161.47 kDa 
• Atom Count: 12,630 
• Modeled Residue Count: 1,419 
• Deposited Residue Count: 1,456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A, B, C, D	364	[Candida] boidinii	Mutation(s): 1  Gene Names: FDH EC: 1.17.1.9
UniProt
Find proteins for A0A0A1EQY0 (Candida boidinii) Explore A0A0A1EQY0  Go to UniProtKB:  A0A0A1EQY0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.664	α = 77.961
b = 68.611	β = 89.626
c = 109.43	γ = 81.402

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-10 
Deposition Author(s): Gul, M., Yuksel, B., Bulut, H., DeMirci, H.

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Funding Organization	Location	Grant Number
Other government	Turkey	--

Revision History  

• Version 1.0: 2023-05-10
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references