6RU9

THE 3D STRUCTURE OF [NIFESE] HYDROGENASE G491A VARIANT FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 1.36 ANGSTROM RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb6RU9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
• Expression System: Nitratidesulfovibrio vulgaris str. Hildenborough
• Mutation(s): Yes 


• Deposited: 2019-05-27 Released: 2019-09-04 
• Deposition Author(s): Matias, P.M., Zacarias, S., Pereita, I.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.163 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 

Literature

A Hydrophilic Channel Is Involved in Oxidative Inactivation of a [NiFeSe] Hydrogenase

Zacarias, S., Temporao, A., del Barrio, M., Fourmond, V., Leger, C., Matias, P.M., Pereira, I.A.C.

(2019) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.9b02347

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: 86.52 kDa 
• Atom Count: 6,745 
• Modelled Residue Count: 759 
• Deposited Residue Count: 775 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic [NiFeSe] hydrogenase, small subunit	A	283	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  Gene Names: hysB, DVU_1917 EC: 1.12.7.2
UniProt
Find proteins for Q72AS4 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72AS4  Go to UniProtKB:  Q72AS4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing	B	492	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 1  Gene Names: hysA, DVU_1918 EC: 1.12.7.2
UniProt
Find proteins for Q72AS3 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72AS3  Go to UniProtKB:  Q72AS3

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6ML	F [auth A]	oxygen-damaged SF4 Fe4 O2 S4 DCVJTSMMUVGUAG-UHFFFAOYSA-M
SF4	C [auth A], D [auth A], E [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
FCO	G [auth B]	CARBONMONOXIDE-(DICYANO) IRON C3 Fe N2 O VBQUCMTXYFMTTE-UHFFFAOYSA-N
GOL	L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	H [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
FE2	I [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
H2S	J [auth B], K [auth B]	HYDROSULFURIC ACID H2 S RWSOTUBLDIXVET-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.163 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.445	α = 90
b = 98.664	β = 105.36
c = 63.885	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
STARANISO	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): Matias, P.M., Zacarias, S., Pereita, I.

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Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BBB-BEP/2885/2014
Fundacao para a Ciencia e a Tecnologia	Portugal	SFRH/BD/100314/2014

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description