9XCW | pdb_00009xcw

Cryo-EM structure of HalM1, a class II lanthipeptide synthetase, bound with substrate, ATP, and Zn

PDB DOI: https://doi.org/10.2210/pdb9XCW/pdb
EM Map EMD-66746: EMDB EMDataResource

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Halalkalibacterium halodurans C-125
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-10-26 Released: 2026-10-28
Deposition Author(s): Gan, B.K., Luo, M.
Funding Organization(s): Ministry of Education (MoE, Singapore)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.19 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of HalM1, a class II lanthipeptide synthetase, bound with substrate, ATP, and Zn

Gan, B.K., Luo, M.

To be published.

Macromolecule Content

Total Structure Weight: 128.6 kDa
Atom Count: 8,047
Modeled Residue Count: 1,004
Deposited Residue Count: 1,128
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lantibiotic mersacidin modifying enzyme	A	1,059	Halalkalibacterium halodurans C-125	Mutation(s): 0 Gene Names: BH0455
UniProt
Find proteins for Q9KFM4 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KFM4 Go to UniProtKB: Q9KFM4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KFM4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lantibiotic mersacidin	B	69	Halalkalibacterium halodurans C-125	Mutation(s): 0 Gene Names: BH0454
UniProt
Find proteins for Q9KFM5 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KFM5 Go to UniProtKB: Q9KFM5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KFM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.19 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education (MoE, Singapore)	Singapore	--

Revision History (Full details and data files)

Version 1.0: 2026-10-28
Type: Initial release