7ZDY

Crystal structure of beta-xylosidase from Thermotoga maritima in complex with methyl-beta-D-xylopyranoside

• PDB DOI: https://doi.org/10.2210/pdb7ZDY/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-03-30 Released: 2023-04-19 
• Deposition Author(s): Gloster, T.M., Foltanyi, F.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.191 
• R-Value Work: 0.172 

Starting Models: experimental

Literature

Structural and further functional characterisation of a glycoside hydrolase family 3 beta-xylosidase from Thermotoga maritima

Gloster, T.M., Foltanyi, F., Hobbs, E.M., Pritchard, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 180.25 kDa 
• Atom Count: 12,874 
• Modelled Residue Count: 1,524 
• Deposited Residue Count: 1,602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylosidase	A [auth W], B [auth Y]	801	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: Tmari_0073 EC: 3.2.1.37 (PDB Primary Data), 3.2.1.21 (UniProt)
UniProt
Find proteins for Q9WXT1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXT1  Go to UniProtKB:  Q9WXT1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6MJ (Subject of Investigation/LOI)	E [auth W], H [auth Y]	methyl beta-D-xylopyranoside C6 H12 O5 ZBDGHWFPLXXWRD-JGWLITMVSA-N
MPD	C [auth W], D [auth W], F [auth Y], G [auth Y]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.191 
• R-Value Work: 0.172 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.62	α = 90
b = 97.68	β = 90
c = 100.69	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Gloster, T.M., Foltanyi, F.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description