9WYA | pdb_00009wya

Structure of a highly active sortase A mutant

• PDB DOI: https://doi.org/10.2210/pdb9WYA/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-09-26 Released: 2026-10-14 
• Deposition Author(s): Heo, Y.-S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for the high acitivity of a penta-mutated sortase A

Heo, Y.-S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.09 kDa 
• Atom Count: 1,284 
• Modeled Residue Count: 147 
• Deposited Residue Count: 150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sortase family protein	A	150	Staphylococcus aureus	Mutation(s): 4  Gene Names: SALFYP88_01125
UniProt
Find proteins for A0A6N3AVW4 (Staphylococcus aureus) Explore A0A6N3AVW4  Go to UniProtKB:  A0A6N3AVW4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.36	α = 90
b = 61.46	β = 90
c = 61.63	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-14 
Deposition Author(s): Heo, Y.-S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-10-14
  Type: Initial release