8JL8

Crystal structure of the collagen binding domain of Cnm from Streptococcus mutans

• PDB DOI: https://doi.org/10.2210/pdb8JL8/pdb

• Classification: PROTEIN BINDING
• Organism(s): Streptococcus mutans
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2023-06-02 Released: 2024-04-10 
• Deposition Author(s): Tanaka, S.-i., Hirata, A., Takano, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.246 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 

Literature

Structure, Stability and Binding Properties of Collagen-Binding Domains from Streptococcus mutans.

Nishi, A., Matsui, H., Hirata, A., Mukaiyama, A., Tanaka, S.-i., Yoshizawa, T., Matsumura, H., Nomura, R., Nakano, K., Takano, K.

(2023) Chemistry 5: 1911-1920

• DOI: https://doi.org/10.3390/chemistry5030130

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: 35.71 kDa 
• Atom Count: 2,405 
• Modelled Residue Count: 291 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen-binding adhesin	A	318	Streptococcus mutans	Mutation(s): 0  Gene Names: cnm
UniProt
Find proteins for B9A878 (Streptococcus mutans) Explore B9A878  Go to UniProtKB:  B9A878

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.246 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.915	α = 90
b = 40.915	β = 90
c = 364.893	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Tanaka, S.-i., Hirata, A., Takano, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	15K15749
Japan Society for the Promotion of Science (JSPS)	Japan	18K09735
Japan Society for the Promotion of Science (JSPS)	Japan	22K10233

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release