9YAA | pdb_00009yaa

Crystal structure of a SnoaL-like domain-containing protein from Mycobacterium ulcerans (Orthorhombic C form)

• PDB DOI: https://doi.org/10.2210/pdb9YAA/pdb

• Classification: ISOMERASE
• Organism(s): Mycobacterium ulcerans Agy99
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-09-15 Released: 2025-09-24 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 
  0.181 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a SnoaL-like domain-containing protein from Mycobacterium ulcerans (Orthorhombic C form)

Liu, L., Lovell, S., Ung, A.R., Buchko, G.W., Battaile, K.P.

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: 17.13 kDa 
• Atom Count: 1,170 
• Modeled Residue Count: 119 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SnoaL-like domain-containing protein	A	146	Mycobacterium ulcerans Agy99	Mutation(s): 0  Gene Names: MUL_2490
UniProt
Find proteins for A0PR67 (Mycobacterium ulcerans (strain Agy99)) Explore A0PR67  Go to UniProtKB:  A0PR67

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.181 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39YAA

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.073	α = 90
b = 71.564	β = 90
c = 56.445	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release