6D4B | pdb_00006d4b

Crystal structure of Candida boidinii formate dehydrogenase V123A mutant complexed with NAD+ and azide

• PDB DOI: https://doi.org/10.2210/pdb6D4B/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): [Candida] boidinii
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2018-04-17 Released: 2019-04-24 
• Deposition Author(s): Guo, Q., Ye, H., Gakhar, L., Cheatum, C.M., Kohen, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.180 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Oscillatory Active-site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase

Pagano, P.L., Guo, Q., Ranasinghe, C., Schroeder, E., Robben, K., Hase, F., Ye, H., Wickersham, K., Aspuru-Guzik, A., Major, D.T., Gakhar, L., Kohen, A., Cheatum, C.M.

(2019) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.9b03345

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 82.16 kDa 
• Atom Count: 6,942 
• Modeled Residue Count: 722 
• Deposited Residue Count: 728 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A, B	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	C [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
AZI (Subject of Investigation/LOI)	D [auth A], G [auth B]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N
CL	E [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.180 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.171	α = 90
b = 116.098	β = 106.84
c = 63.088	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
XDS	data scaling
Coot	model building
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Guo, Q., Ye, H., Gakhar, L., Cheatum, C.M., Kohen, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM079368

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description