6SG2 | pdb_00006sg2

FeFe Hydrogenase from Nitratidesulfovibrio vulgaris in Hinact state

• PDB DOI: https://doi.org/10.2210/pdb6SG2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nitratidesulfovibrio vulgaris, Desulfovibrio desulfuricans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-02 Released: 2020-07-08 
• Deposition Author(s): Galle, L.M., Span, I.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.212 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.172 (DCC) 

Starting Model: experimental

Literature

Caught in the H inact : Crystal Structure and Spectroscopy Reveal a Sulfur Bound to the Active Site of an O 2 -stable State of [FeFe] Hydrogenase.

Rodriguez-Macia, P., Galle, L.M., Bjornsson, R., Lorent, C., Zebger, I., Yoda, Y., Cramer, S.P., DeBeer, S., Span, I., Birrell, J.A.

(2020) Angew Chem Int Ed Engl 59: 16786-16794

• PubMed: 32488975 
• DOI: https://doi.org/10.1002/anie.202005208
• Primary Citation Related Structures: 
  6SG2


• PubMed Abstract: 
  

  [FeFe] hydrogenases are the most active H ₂ converting catalysts in nature, but their extreme oxygen sensitivity limits their use in technological applications. The [FeFe] hydrogenases from sulfate reducing bacteria can be purified in an O ₂ -stable state called H _inact . To date, the structure and mechanism of formation of H _inact remain unknown. Our 1.65 Å crystal structure of this state reveals a sulfur ligand bound to the open coordination site. Furthermore, in-depth spectroscopic characterization by X-ray absorption spectroscopy (XAS), nuclear resonance vibrational spectroscopy (NRVS), resonance Raman (RR) spectroscopy and infrared (IR) spectroscopy, together with hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, provide detailed chemical insight into the H _inact state and its mechanism of formation. This may facilitate the design of O ₂ -stable hydrogenases and molecular catalysts.

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Organizational Affiliation: 
• Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany.
Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK.
Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
Physikalische Chemie/ Biophysikalische Chemie, Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
Japanese Synchrotron Radiation Institute, Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo, 679-5198, Japan.
SETI Institute, 189 Bernardo Avenue, Mountain View, California, 94043, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 54.75 kDa 
• Atom Count: 3,936 
• Modeled Residue Count: 484 
• Deposited Residue Count: 484 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic [Fe] hydrogenase large subunit	A [auth AAA]	396	Nitratidesulfovibrio vulgaris	Mutation(s): 0  Gene Names: hydA, DDE01_08480

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HydB	B [auth BBB]	88	Desulfovibrio desulfuricans	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LFH (Subject of Investigation/LOI)	F [auth AAA]	dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) sulphide C7 H5 Fe2 N3 O3 S3 VVXMKEXCTCBOII-UHFFFAOYSA-L
SF4	C [auth AAA], D [auth AAA], E [auth AAA]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.212 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.172 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.34	α = 90
b = 86.82	β = 90
c = 88.17	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Galle, L.M., Span, I.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SP 1476/4-1

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2020-09-30
  Changes: Database references
• Version 1.2: 2020-12-16
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2026-02-25
  Changes: Source and taxonomy, Structure summary