7WDP | pdb_00007wdp

Crystal structures of MeBglD2 in complex with various saccharides

• PDB DOI: https://doi.org/10.2210/pdb7WDP/pdb

• Classification: HYDROLASE
• Organism(s): metagenome
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-12-22 Released: 2022-11-02 
• Deposition Author(s): Watanabe, M., Matsuzawa, T., Nakamichi, Y., Akita, H., Yaoi, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of metagenomic beta-glycosidase MeBglD2 in complex with various saccharides

Matsuzawa, T., Watanabe, M., Nakamichi, Y., Akita, H., Yaoi, K.

(2022) Appl Microbiol Biotechnol 106: 4539-4551

• DOI: https://doi.org/10.1007/s00253-022-12018-6

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.8 kDa 
• Atom Count: 3,780 
• Modeled Residue Count: 445 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A	458	metagenome	Mutation(s): 0  EC: 3.2.1.21
UniProt
Find proteins for A0A1E1FFN6 (uncultured microorganism) Explore A0A1E1FFN6  Go to UniProtKB:  A0A1E1FFN6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC (Subject of Investigation/LOI)	C [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
SO4 (Subject of Investigation/LOI)	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.842	α = 90
b = 201.842	β = 90
c = 201.842	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-02 
Deposition Author(s): Watanabe, M., Matsuzawa, T., Nakamichi, Y., Akita, H., Yaoi, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2022-11-02
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description