8W7L | pdb_00008w7l

Cryo-EM structure of ClassIII Lanthipeptide modification enzyme PneKC mutant H522A.

• PDB DOI: https://doi.org/10.2210/pdb8W7L/pdb
• EM Map EMD-37340: EMDB EMDataResource

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-08-30 Released: 2024-09-04 
• Deposition Author(s): Li, Y., Luo, M., Shao, K., Li, J., Li, Z.
• Funding Organization(s): Ministry of Education (MoE, Singapore)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of PneA bound PneKC at 3.75 Angstroms resolution.

Li, Y., Luo, M., Shao, K., Li, J., Li, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 204.1 kDa 
• Atom Count: 13,579 
• Modeled Residue Count: 1,745 
• Deposited Residue Count: 1,766 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein kinase domain-containing protein	A	866	Streptococcus pneumoniae	Mutation(s): 1  Gene Names: SPRM200_1177
UniProt
Find proteins for A0A2U3S0J5 (Streptococcus pneumoniae) Explore A0A2U3S0J5  Go to UniProtKB:  A0A2U3S0J5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein kinase domain-containing protein	B	865	Streptococcus pneumoniae	Mutation(s): 1  Gene Names: SPRM200_1177
UniProt
Find proteins for A0A2U3S0J5 (Streptococcus pneumoniae) Explore A0A2U3S0J5  Go to UniProtKB:  A0A2U3S0J5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PneA	C	18	Streptococcus pneumoniae	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PneA	D	17	Streptococcus pneumoniae	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	E [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Li, Y., Luo, M., Shao, K., Li, J., Li, Z.

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

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 2.0: 2024-11-06
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2025-07-02
  Changes: Data collection