8DZD | pdb_00008dzd

Structure of MS3494 from Mycobacterium smegmatis bound to sucrose

• PDB DOI: https://doi.org/10.2210/pdb8DZD/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-08-06 Released: 2023-08-09 
• Deposition Author(s): Kent, J.E., Aleshin, A.E., Marassi, F.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.147 (DCC) 

Starting Model: experimental

Literature

Structure of MS3494 from Mycobacterium smegmatis bound to sucrose

Kent, J.E., Aleshin, A.E., Marassi, F.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.9 kDa 
• Atom Count: 2,292 
• Modeled Residue Count: 243 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MS3494	A, B	127	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_3494
UniProt
Find proteins for A0QY10 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QY10  Go to UniProtKB:  A0QY10

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C, D	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.147 (DCC) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.463	α = 90
b = 98.463	β = 90
c = 45.581	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Kent, J.E., Aleshin, A.E., Marassi, F.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description