9XHF | pdb_00009xhf

ancestral sortase E 2

• PDB DOI: https://doi.org/10.2210/pdb9XHF/pdb

• Classification: HYDROLASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-10-31 Released: 2026-11-04 
• Deposition Author(s): Chisuga, T., Koshiba, R., Nakano, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.205 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: in silico

Literature

Screening and Engineering of Ancestral Sortase Es that Enable High-Fidelity Enzyme Design with Activity Trade-off

Koshiba, R., Chisga, T., Takeda, H., Nakano, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17 kDa 
• Atom Count: 1,203 
• Modeled Residue Count: 151 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class E sortase	A	158	synthetic construct	Mutation(s): 0  Gene Names: GCM10010430_52820
UniProt
Find proteins for A0ABN3ELD4 (Kitasatospora cystarginea) Explore A0ABN3ELD4  Go to UniProtKB:  A0ABN3ELD4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.205 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.731	α = 90
b = 36.731	β = 90
c = 184.361	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-04 
Deposition Author(s): Chisuga, T., Koshiba, R., Nakano, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	24H01153
Japan Society for the Promotion of Science (JSPS)	Japan	25H01420
Japan Society for the Promotion of Science (JSPS)	Japan	25H01588
Japan Society for the Promotion of Science (JSPS)	Japan	24K17828
Japan Society for the Promotion of Science (JSPS)	Japan	25H01589
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ae0121018
Japan Science and Technology	Japan	JPMJPR20AB
Japan Science and Technology	Japan	JPMJAN25D1

Revision History  

• Version 1.0: 2026-11-04
  Type: Initial release