9IOK | pdb_00009iok

Crystal Structure of Sortase E from Thermobifida fusca

• PDB DOI: https://doi.org/10.2210/pdb9IOK/pdb

• Classification: HYDROLASE
• Organism(s): Thermobifida fusca YX
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-09 Released: 2025-07-09 
• Deposition Author(s): Sharma, V., Murmu, S., Megta, A., Roy, R.P., Krishnan, V.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.196 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Analysis of Sortase E from Thermobifida fusca

Sharma, V., Murmu, S., Megta, A., Roy, R.P., Krishnan, V.

To be published.

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: 40.98 kDa 
• Atom Count: 2,859 
• Modeled Residue Count: 342 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase C60, sortase A and B	A, B	181	Thermobifida fusca YX	Mutation(s): 0  Gene Names: Tfu_2383
UniProt
Find proteins for Q47MA6 (Thermobifida fusca (strain YX)) Explore Q47MA6  Go to UniProtKB:  Q47MA6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO (Subject of Investigation/LOI)	C [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	D [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA (Subject of Investigation/LOI)	E [auth A], F [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.196 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.111	α = 90
b = 111.111	β = 90
c = 70.023	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Sharma, V., Murmu, S., Megta, A., Roy, R.P., Krishnan, V.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release