7W2T

Crystal structure of TxGH116 E730Q mutant from Thermoanaerobacterium xylanolyticum with glucose

• PDB DOI: https://doi.org/10.2210/pdb7W2T/pdb

• Classification: HYDROLASE
• Organism(s): Thermoanaerobacterium xylanolyticum LX-11
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-11-24 Released: 2022-04-06 
• Deposition Author(s): Huang, M., Pengthaisong, S., Charoenwattanasatien, R., Jitonnom, J., Ketudat Cairns, J.R.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.203 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Starting Model: experimental

Literature

Systematic Functional and Computational Analysis of Glucose-Binding Residues in Glycoside Hydrolase Family GH116.

Huang, M., Pengthaisong, S., Charoenwattanasatien, R., Thinkumrob, N., Jitonnom, J., Ketudat Cairns, J.R.

(2022) Catalysts 12

• DOI: https://doi.org/10.3390/catal12030343

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: 194.27 kDa 
• Atom Count: 13,117 
• Modelled Residue Count: 1,544 
• Deposited Residue Count: 1,684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosylceramidase	A, B	842	Thermoanaerobacterium xylanolyticum LX-11	Mutation(s): 1  Gene Names: Thexy_2211 EC: 3.2.1.45
UniProt
Find proteins for F6BL85 (Thermoanaerobacterium xylanolyticum (strain ATCC 49914 / DSM 7097 / LX-11)) Explore F6BL85  Go to UniProtKB:  F6BL85

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC (Subject of Investigation/LOI)	C [auth A], J [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	I [auth A], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.203 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.377	α = 90
b = 124.458	β = 90
c = 174.263	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Huang, M., Pengthaisong, S., Charoenwattanasatien, R., Jitonnom, J., Ketudat Cairns, J.R.

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Funding Organization	Location	Grant Number
Other government	Thailand	Suranaree University of Technology
Other government	Thailand	Thailand Research Fund
Other government	Thailand	Thailand Science Research and Innovation
Other government	Thailand	Synchrotron Light Research Institute (Public Organization)
Other government	Thailand	University of Phayao

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description