3QOM

Crystal structure of 6-phospho-beta-glucosidase from Lactobacillus plantarum

• PDB DOI: https://doi.org/10.2210/pdb3QOM/pdb

• Classification: HYDROLASE
• Organism(s): Lactiplantibacillus plantarum
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-02-10 Released: 2011-03-09 
• Deposition Author(s): Michalska, K., Hatzos-Skintges, C., Bearden, J., Kohler, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.134 
• R-Value Work: 0.118 
• R-Value Observed: 0.118 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.42 kDa 
• Atom Count: 4,627 
• Modelled Residue Count: 479 
• Deposited Residue Count: 481 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phospho-beta-glucosidase	A	481	Lactiplantibacillus plantarum	Mutation(s): 0  Gene Names: pbg1, lp_0440 EC: 3.2.1.86
UniProt
Find proteins for F9UU25 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9UU25  Go to UniProtKB:  F9UU25

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	B [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
PO4	C [auth A], D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.134 
• R-Value Work: 0.118 
• R-Value Observed: 0.118 
• Space Group: P 6 2 2
• Diffraction Data: https://doi.org/10.18430/M33QOM

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.647	α = 90
b = 150.647	β = 90
c = 95.9	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-09 
Deposition Author(s): Michalska, K., Hatzos-Skintges, C., Bearden, J., Kohler, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-07-02
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary