30GJ | pdb_000030gj

W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - Ambient temperature, Serial crystallography

• PDB DOI: https://doi.org/10.2210/pdb30GJ/pdb

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


• Deposited: 2026-04-23 Released: 2026-08-19 
• Deposition Author(s): Vilela-Alves, G., Martins, G., von Stetten, D., Mehrabi, P., Pereira, I.C., Romao, M.J., Pearson, A.R., Mota, C.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.222 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Room-temperature crystal structure of a metal-dependent W-formate dehydrogenase by serial synchrotron crystallography.

Vilela-Alves, G., Martins, G., von Stetten, D., Mehrabi, P., Pereira, I.A.C., Romao, M.J., Pearson, A.R., Mota, C.

(2026) Acta Crystallogr D Struct Biol 

• PubMed: 42572941 
• DOI: https://doi.org/10.1107/S2059798326006923
• Primary Citation Related Structures: 
  30GJ, 30GK


• PubMed Abstract: 
  

  Metal-dependent formate dehydrogenases (Fdhs) are a promising research target in efforts to mitigate climate change by developing active, efficient, selective and safe industrial catalysts for CO ₂ reduction. Here, we report the room-temperature (RT) serial synchrotron X-ray crystallography (SSX) structure of Nitratidesulfovibrio vulgaris formate dehydrogenase AB and compare this structure with previously reported cryogenic structures. The comparison reveals structural differences likely arising from the absence of cryoprotectants, differences in data-collection temperature and the much lower radiation dose accumulated by each crystal during the SSX experiments. The RT-SSX structure provides the first step towards time-resolved serial crystallography experiments targeting possible catalytic intermediates in order to fully understand the catalytic mechanism of metal-dependent Fdhs.

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Organizational Affiliation: 
• Associate Laboratory i4HB - Institute for Health and Bioeconomy and UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal.
European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Institute for Nanostructure and Solid-State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 139.53 kDa 
• Atom Count: 9,663 
• Modeled Residue Count: 1,179 
• Deposited Residue Count: 1,228 
• 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	215	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 4 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], H [auth B], I [auth B], J [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
W (Subject of Investigation/LOI)	G [auth A]	TUNGSTEN ION W FZFRVZDLZISPFJ-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: 1.93 Å
• R-Value Free:  0.222 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.5	α = 90
b = 129.6	β = 90
c = 151.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-19 
Deposition Author(s): Vilela-Alves, G., Martins, G., von Stetten, D., Mehrabi, P., Pereira, I.C., Romao, M.J., Pearson, A.R., 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	doi.org/10.54499/2023.00286.BD
Fundacao para a Ciencia e a Tecnologia	Portugal	doi.org/10.54499/UID/04378/2025
Fundacao para a Ciencia e a Tecnologia	Portugal	doi.org/10.54499/UID/PRR/04378/2025
Fundacao para a Ciencia e a Tecnologia	Portugal	doi.org/10.54499/LA/P/0140/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	LA/P/0087/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDB/04612/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDP/04612/2020

Revision History  

• Version 1.0: 2026-08-19
  Type: Initial release