5DO8

1.8 Angstrom crystal structure of Listeria monocytogenes Lmo0184 alpha-1,6-glucosidase

• PDB DOI: https://doi.org/10.2210/pdb5DO8/pdb

• Classification: HYDROLASE
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-10 Released: 2015-09-30 
• Deposition Author(s): Light, S.H., Halavaty, A.S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.188 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 197.32 kDa 
• Atom Count: 15,741 
• Modelled Residue Count: 1,656 
• Deposited Residue Count: 1,665 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo0184 protein	A [auth B], B [auth A], C	555	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: lmo0184
UniProt
Find proteins for Q8YAE6 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8YAE6  Go to UniProtKB:  Q8YAE6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	F [auth B], I [auth A], M [auth C]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
BGC	D [auth B], G [auth A], J [auth C]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
CL	E [auth B], H [auth A], K [auth C], L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.188 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/m35do8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.123	α = 90
b = 103.937	β = 90
c = 193.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Light, S.H., Halavaty, A.S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2016-11-23
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary