8YYN

Crystal structure of TsaGH11 complexed with beta-D-xylopyranose (Data I)

• PDB DOI: https://doi.org/10.2210/pdb8YYN/pdb

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


• Deposited: 2024-04-04 Released: 2024-04-17 
• 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: 1.90 Å
• R-Value Free: 0.207 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

Crystal structure of TsaGH11 complexed with beta-D-xylopyranose (Data I)

Nam, K.H.

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: 40.75 kDa 
• Atom Count: 3,172 
• Modelled Residue Count: 366 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A, B	184	Thermoanaerobacterium saccharolyticum	Mutation(s): 0  Gene Names: Tsac_0897
UniProt
Find proteins for I3VTR8 (Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485)) Explore I3VTR8  Go to UniProtKB:  I3VTR8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYP (Subject of Investigation/LOI)	C [auth A], F [auth B]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N
ACT	D [auth A], E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.207 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.098	α = 90
b = 73.098	β = 90
c = 165.098	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
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: 2024-04-17
  Type: Initial release