9HE2 | pdb_00009he2

Crystal structure of CyuA C289A mutant from Methanococcus maripaludis with [4Fe-4S] clusters in complex with ethylene glycol

PDB DOI: https://doi.org/10.2210/pdb9HE2/pdb

Classification: LYASE
Organism(s): Methanococcus maripaludis S2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-11-13 Released: 2025-11-05
Deposition Author(s): Gervason, S., Pecqueur, L., Golinelli-Pimpaneau, B.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.74 Å
R-Value Free:
0.263 (Depositor), 0.263 (DCC)
R-Value Work:
0.217 (Depositor), 0.217 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: in silico
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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

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

Golinelli-Pimpaneau, B.

To be published.

Macromolecule Content

Total Structure Weight: 88.54 kDa
Atom Count: 5,979
Modeled Residue Count: 776
Deposited Residue Count: 800
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-cysteine desulfidase	A, B	400	Methanococcus maripaludis S2	Mutation(s): 1 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 (Subject of Investigation/LOI) 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]
EDO (Subject of Investigation/LOI) Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		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: 3.74 Å
R-Value Free: 0.263 (Depositor), 0.263 (DCC)
R-Value Work: 0.217 (Depositor), 0.217 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.632	α = 90
b = 74.632	β = 90
c = 251.059	γ = 120

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
STARANISO	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Golinelli-Pimpaneau, B.

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-11-labx-0011
Agence Nationale de la Recherche (ANR)	France	ANR-22-CE44-0012

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release

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.