8RYH | pdb_00008ryh

Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a linker peptide derived from a group A1 type [FeFe]-hydrogenase of Veillonella atypica

• PDB DOI: https://doi.org/10.2210/pdb8RYH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Desulfovibrio desulfuricans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-08 Released: 2025-02-19 
• Deposition Author(s): Bikbaev, K., Jaenecke, J., Winkler, M., Span, I.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.206 (DCC) 

Starting Model: experimental

Literature

Enhancing maturation of [FeFe]-hydrogenase by interlinking the large and small subunits

Bikbaev, K., Jaenecke, J., Winkler, M., Span, I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 55.47 kDa 
• Atom Count: 3,779 
• Modeled Residue Count: 469 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit	A	490	Desulfovibrio desulfuricans	Mutation(s): 0  Gene Names: hydA, DVU_1769, hydB, DVU_1770 EC: 1.12.7.2
UniProt
Find proteins for P07598 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P07598  Go to UniProtKB:  P07598
Find proteins for P07603 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P07603  Go to UniProtKB:  P07603
UniProt Groups	P07603P07598

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
402 (Subject of Investigation/LOI)	E [auth A]	dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) C7 H5 Fe2 N3 O3 S2 LJPDYWPSPOWMIB-UHFFFAOYSA-N
SF4 (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.206 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.118	α = 90
b = 50.603	β = 105.331
c = 86.643	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BUCCANEER	model building
Coot	model building
PHASER	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Bikbaev, K., Jaenecke, J., Winkler, M., Span, I.

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

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release