9M6Y | pdb_00009m6y

Crystal structure of C1 domain from surface protein SlpM of Lactobacillus brevis

• PDB DOI: https://doi.org/10.2210/pdb9M6Y/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Levilactobacillus brevis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-08 Released: 2025-06-11 
• Deposition Author(s): Xue, Y., Kang, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of the C1 domain of the surface-layer protein SlpM from Lactobacillus brevis: a module involved in protein self-assembly.

Xue, Y., Kang, X.

(2025) Acta Crystallogr F Struct Biol Commun 81: 255-262

• PubMed: 40371669 
• DOI: https://doi.org/10.1107/S2053230X25004194
• Primary Citation Related Structures: 
  9M6Y


• PubMed Abstract: 
  

  Surface-layer proteins (SLPs) play a crucial role in the self-assembly of bacterial surface layers, yet the structural details of their assembly domains remain largely unexplored. Here, we report the crystal structure of SlpM_C1, a structural module within the self-assembly domain of SlpM from Lactobacillus brevis. SlpM_C1 adopts a β-grasp fold, a conserved structural motif found in diverse protein families. Structural comparisons with ubiquitin and the SlpA_II domain from L. acidophilus reveal both shared and distinct features, highlighting elements of structural convergence despite sequence divergence. Furthermore, the dimerization patterns of SlpM_C1 and SlpA_II are compared and discussed. These findings provide new insights into the architecture and evolutionary adaptability of SLPs in Lactobacillus species.

---

Organizational Affiliation: 
• Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.27 kDa 
• Atom Count: 1,769 
• Modeled Residue Count: 184 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface layer protein SlpM	A, B	92	Levilactobacillus brevis	Mutation(s): 0  Gene Names: slpM
UniProt
Find proteins for H9BQS1 (Levilactobacillus brevis) Explore H9BQS1  Go to UniProtKB:  H9BQS1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.065	α = 85.85
b = 37.804	β = 84.92
c = 42.058	γ = 66.91

Software Package:

Software Name	Purpose
PHENIX	refinement
SAINT	data scaling
SAINT	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Xue, Y., Kang, X.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release