9FYI | pdb_00009fyi

[4Fe-4S] Cluster-Containing L-Cysteine Desulfidase CyuA from Methanococcus maripaludis

PDB DOI: https://doi.org/10.2210/pdb9FYI/pdb

Classification: TRANSFERASE
Organism(s): Methanococcus maripaludis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-03 Released: 2025-07-16
Deposition Author(s): Zecchin, P., Pecqueur, L., Golinelli, B.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free:
0.261 (Depositor), 0.265 (DCC)
R-Value Work:
0.222 (Depositor), 0.225 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: in silico
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Literature

Insights into the phylogenetic distribution, structure and function of [4Fe-4S]-dependent L-cysteine desulfidase, an enzyme that supplies sulfide to the archaeon Methanococcus maripaludis

Zecchin, P., Golinelli, B.

To be published.

Macromolecule Content

Total Structure Weight: 88.67 kDa
Atom Count: 5,641
Modeled Residue Count: 738
Deposited Residue Count: 800
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-cysteine desulfidase	A, B	400	Methanococcus maripaludis	Mutation(s): 0 Gene Names: MMP1468 EC: 4.4.1.28
UniProt
Find proteins for Q6LX84 (Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL)) Explore Q6LX84 Go to UniProtKB: Q6LX84
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6LX84
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free: 0.261 (Depositor), 0.265 (DCC)
R-Value Work: 0.222 (Depositor), 0.225 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.121	α = 90
b = 79.148	β = 90
c = 156.38	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
PHASES	phasing
BUSTER	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-11-LABX-0011

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.