3WR5 | pdb_00003wr5

Structural basis on the efficient CO2 reduction of acidophilic formate dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb3WR5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thiobacillus sp. KNK65MA
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-02-16 Released: 2015-02-25 
• Deposition Author(s): Ha, J.M., Jeon, S.T., Yoon, H.J., Lee, H.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Structural basis on the efficient CO2 reduction of acidophilic formate dehydrogenase

Ha, J.M., Jeon, S.T., Yoon, H.J., Lee, H.H.

To be published.

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 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: 179.92 kDa 
• Atom Count: 13,250 
• Modeled Residue Count: 1,569 
• Deposited Residue Count: 1,624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A, B, C, D	406	Thiobacillus sp. KNK65MA	Mutation(s): 0  Gene Names: fdh65MA EC: 1.2.1.2 (PDB Primary Data), 1.17.1.9 (UniProt)
UniProt
Find proteins for Q76EB7 (Thiobacillus sp. KNK65MA) Explore Q76EB7  Go to UniProtKB:  Q76EB7

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.942	α = 90
b = 72.729	β = 90
c = 386.767	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
DENZO	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-25 
Deposition Author(s): Ha, J.M., Jeon, S.T., Yoon, H.J., Lee, H.H.

Revision History  

• Version 1.0: 2015-02-25
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description