6SDR

W-formate dehydrogenase from Desulfovibrio vulgaris - Oxidized form

• PDB DOI: https://doi.org/10.2210/pdb6SDR/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
• Mutation(s): No 


• Deposited: 2019-07-29 Released: 2020-03-11 
• Deposition Author(s): Oliveira, A.R., Mota, C., Mourato, C., Domingos, R.M., Santos, M.F.A., Gesto, D., Guigliarelli, B., Santos-Silva, T., Romao, M.J., Pereira, I.C.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.226 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Towards the mechanistic understanding of enzymatic CO2 reduction

Oliveira, A.R., Mota, C., Mourato, C., Domingos, R.M., Santos, M.F.A., Gesto, D., Guigliarelli, B., Santos-Silva, T., Romao, M.J., Pereira, I.C.

(2020) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.0c00086

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 141.44 kDa 
• Atom Count: 9,959 
• Modelled Residue Count: 1,177 
• Deposited Residue Count: 1,241 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase, alpha subunit, selenocysteine-containing	A	1,005	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  EC: 1.2.1.2
UniProt
Find proteins for Q72EJ1 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72EJ1  Go to UniProtKB:  Q72EJ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase, beta subunit, putative	B	236	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0
UniProt
Find proteins for Q72EJ0 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72EJ0  Go to UniProtKB:  Q72EJ0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGD (Subject of Investigation/LOI)	C [auth A], D [auth A]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C20 H26 N10 O13 P2 S2 VQAGYJCYOLHZDH-ILXWUORBSA-N
SF4	E [auth A], M [auth B], N [auth B], O [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
W (Subject of Investigation/LOI)	L [auth A]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
H2S (Subject of Investigation/LOI)	K [auth A]	HYDROSULFURIC ACID H2 S RWSOTUBLDIXVET-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.226 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.593	α = 90
b = 127.644	β = 90
c = 148.213	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-11 
Deposition Author(s): Oliveira, A.R., Mota, C., Mourato, C., Domingos, R.M., Santos, M.F.A., Gesto, D., Guigliarelli, B., Santos-Silva, T., Romao, M.J., Pereira, I.C.

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Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BBB-EBB/2723/2014
Fundacao para a Ciencia e a Tecnologia	Portugal	UID/Multi/04378/2019

Revision History  

• Version 1.0: 2020-03-11
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary