9FSL | pdb_00009fsl

Crystal structure of CyuA from Methanococcus maripaludis with [2Fe-2S] clusters solved by Fe-SAD

• PDB DOI: https://doi.org/10.2210/pdb9FSL/pdb

• Classification: LYASE
• Organism(s): Methanococcus maripaludis S2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-21 Released: 2025-07-02 
• Deposition Author(s): Pecqueur, L., He, N., Golinelli-Pimpaneau, B.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.276 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

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

Golinelli-Pimpaneau, B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 88.36 kDa 
• Atom Count: 5,676 
• Modeled Residue Count: 736 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-cysteine desulfidase	A, B	400	Methanococcus maripaludis S2	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES (Subject of Investigation/LOI)	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)	C [auth A], E [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
CL	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.276 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.166	α = 90
b = 77.226	β = 90
c = 153.969	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
BUSTER	refinement
PHASER	phasing
PARROT	phasing
CRANK2	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Pecqueur, L., He, N., Golinelli-Pimpaneau, B.

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

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release