6M6L | pdb_00006m6l

The crystal structure of glycosidase hydrolyzing Notoginsenoside

• PDB DOI: https://doi.org/10.2210/pdb6M6L/pdb

• Classification: HYDROLASE
• Organism(s): Kribbella flavida DSM 17836
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-03-15 Released: 2021-03-17 
• Deposition Author(s): Wang, R.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.174 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Characterization and Structural Elucidation of Enhanced Catalytic Activity upon Engineering Glycosidase KfGH01 for the Production of Vina-ginsenoside R7

Wang, R.F.

To be published.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 99.15 kDa 
• Atom Count: 8,224 
• Modeled Residue Count: 892 
• Deposited Residue Count: 894 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A, B	447	Kribbella flavida DSM 17836	Mutation(s): 0  Gene Names: Kfla_5268 EC: 3.2.1.21
UniProt
Find proteins for D2PL27 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PL27  Go to UniProtKB:  D2PL27

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYP (Subject of Investigation/LOI)	G [auth B]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N
GOL (Subject of Investigation/LOI)	C [auth A], D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.174 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.608	α = 90
b = 95.571	β = 90.65
c = 93.348	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Wang, R.F.

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description