9K72 | pdb_00009k72

Crystal structure of TsaBgl using merged datasets

• PDB DOI: https://doi.org/10.2210/pdb9K72/pdb

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


• Deposited: 2024-10-23 Released: 2024-11-06 
• Deposition Author(s): Nam, K.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Application of Serial Crystallography for Merging Incomplete Macromolecular Crystallography Datasets.

Nam, K.H.

(2024) Crystals (Basel) 14

• DOI: https://doi.org/10.3390/cryst14121012

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: 52.03 kDa 
• Atom Count: 4,230 
• Modeled Residue Count: 444 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-glucosidase	A	444	Thermoanaerobacterium saccharolyticum	Mutation(s): 0  Gene Names: Tsac_2208 EC: 3.2.1.21
UniProt
Find proteins for I3VXG7 (Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485)) Explore I3VXG7  Go to UniProtKB:  I3VXG7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
NA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.21	α = 90
b = 71.12	β = 90
c = 99.49	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Nam, K.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1I1A1A01050838

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Database references