8RU6 | pdb_00008ru6

Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 4 amino acid linker peptide derived from CpI of Clostridium pasteurianum

PDB DOI: https://doi.org/10.2210/pdb8RU6/pdb

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

Deposited: 2024-01-30 Released: 2025-02-12
Deposition Author(s): Bikbaev, K., Jaenecke, J., Winkler, M., Span, I.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.158 (Depositor), 0.158 (DCC)
R-Value Work:
0.137 (Depositor), 0.137 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 56.49 kDa
Atom Count: 4,365
Modeled Residue Count: 484
Deposited Residue Count: 491
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic [Fe] hydrogenase large subunit,CpI,Periplasmic [Fe] hydrogenase small subunit	A [auth B]	491	Desulfovibrio desulfuricans, Clostridium pasteurianum	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
Find proteins for P29166 (Clostridium pasteurianum) Explore P29166 Go to UniProtKB: P29166
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P07603P07598P29166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MHX (Subject of Investigation/LOI) Query on MHX Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) C₈ H₅ Fe₂ N₃ O₄ S₂ HQBPXMLEPWPPEN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	F [auth B], G [auth B], H [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain B SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain B MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] mmCIF format, chain B mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B]	B, C [auth B], D [auth B], E [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain B Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain B Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B]