8RCA

W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Reoxidized by exposure to air for 1 h in the absence of Formate

• PDB DOI: https://doi.org/10.2210/pdb8RCA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
• Expression System: Nitratidesulfovibrio vulgaris str. Hildenborough
• Mutation(s): No 


• Deposited: 2023-12-06 Released: 2024-07-24 
• Deposition Author(s): Vilela-Alves, G., Manuel, R.R., Pereira, I.C., Romao, M.J., Mota, C.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.232 
• R-Value Work: 0.194 

Starting Model: experimental

Literature

Substrate-dependent oxidative inactivation of a W-dependent formate dehydrogenase involving selenocysteine displacement

Vilela-Alves, G., Manuel, R.R., Viegas, A., Carpentier, P., Biaso, F., Guigliarelli, B., Pereira, I.C., Romao, M.J., Mota, C.

(2024) Chem Sci 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 140.02 kDa 
• Atom Count: 9,971 
• Modelled Residue Count: 1,181 
• Deposited Residue Count: 1,227 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase, alpha subunit, selenocysteine-containing	A	1,013	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  Gene Names: fdnG-1, DVU_0587 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	214	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  Gene Names: DVU_0588
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 6 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 (Subject of Investigation/LOI)	E [auth A], N [auth B], O [auth B], P [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
W (Subject of Investigation/LOI)	G [auth A]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N
GOL	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	M [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
H2S (Subject of Investigation/LOI)	F [auth A]	HYDROSULFURIC ACID H2 S RWSOTUBLDIXVET-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.232 
• R-Value Work: 0.194 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.51093/xrd-00181
• Diffraction Data: https://doi.org/10.15151/ESRF-ES-541100365

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.558	α = 90
b = 128.006	β = 90
c = 148.905	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
STARANISO	data scaling
PHASER	phasing
XDS	data reduction
Aimless	data scaling
XSCALE	data scaling
pointless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Vilela-Alves, G., Manuel, R.R., Pereira, I.C., Romao, M.J., Mota, C.

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Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BII-BBF/2050/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDP/04378/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDB/04378/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDB/04612/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDP/04612/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	LA/P/0140/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	LA/P/0087/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	2023.00286.BD

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release