4ZO7

Crystal structure of mutant (D270A) beta-glucosidase from Listeria innocua in complex with gentiobiose

• PDB DOI: https://doi.org/10.2210/pdb4ZO7/pdb

• Classification: HYDROLASE
• Organism(s): Listeria innocua Clip11262
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-05-06 Released: 2016-05-18 
• Deposition Author(s): Nakajima, M., Yoshida, R., Miyanaga, A., Abe, K., Takahashi, Y., Sugimoto, N., Toyoizumi, H., Nakai, H., Kitaoka, M., Taguchi, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.163 
• R-Value Observed: 0.166 

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)

Macromolecule Content

• Total Structure Weight: 162.35 kDa 
• Atom Count: 12,076 
• Modelled Residue Count: 1,448 
• Deposited Residue Count: 1,462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lin1840 protein	A, B	731	Listeria innocua Clip11262	Mutation(s): 2  Gene Names: lin1840
UniProt
Find proteins for Q92AS9 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q92AS9  Go to UniProtKB:  Q92AS9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-6)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G91215DP GlyCosmos:  G91215DP

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	I [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
BGC	D [auth A], E [auth A], H [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	F [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.163 
• R-Value Observed: 0.166 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.6	α = 90
b = 95.16	β = 96.38
c = 215.404	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Nakajima, M., Yoshida, R., Miyanaga, A., Abe, K., Takahashi, Y., Sugimoto, N., Toyoizumi, H., Nakai, H., Kitaoka, M., Taguchi, H.

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references
• Version 1.2: 2020-02-19
  Changes: Data collection, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary