6VC6

2.1 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Gut Microorganisms in Complex with NAD and Mn2+

• PDB DOI: https://doi.org/10.2210/pdb6VC6/pdb

• Classification: HYDROLASE
• Organism(s): Merdibacter massiliensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-12-20 Released: 2020-12-23 
• Deposition Author(s): Wu, R., Kim, Y., Endres, M., Joachimiak, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

2.1 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Gut Microorganisms in Complex with NAD and Mn2+

Wu, R., Kim, Y., Endres, M., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 211.17 kDa 
• Atom Count: 14,988 
• Modelled Residue Count: 1,743 
• Deposited Residue Count: 1,764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phospho-alpha-glucosidase	A, B, C, D	441	Merdibacter massiliensis	Mutation(s): 0  Gene Names: AGLB EC: 3.2.1.122

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	G [auth A], J [auth B], N [auth C], S [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
G6P (Subject of Investigation/LOI)	F [auth A], I [auth B], M [auth C], R [auth D]	6-O-phosphono-alpha-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-DVKNGEFBSA-N
GOL	K [auth B], O [auth C], P [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	E [auth A], H [auth B], L [auth C], Q [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.46	α = 90
b = 62.257	β = 90.35
c = 160.706	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Wu, R., Kim, Y., Endres, M., Joachimiak, J.

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection