8C7F | pdb_00008c7f

Crystal structure of beta-xylosidase mutant (D281N, E517Q) from Thermotoga maritima in complex with xylopentaose

• PDB DOI: https://doi.org/10.2210/pdb8C7F/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-01-15 Released: 2024-01-24 
• Deposition Author(s): Gloster, T.M., Foltanyi, F.
• Funding Organization(s): Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.189 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

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

Gloster, T.M., Foltanyi, F.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 175.41 kDa 
• Atom Count: 13,340 
• Modeled Residue Count: 1,511 
• Deposited Residue Count: 1,560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylosidase	A, B	780	Thermotoga maritima MSB8	Mutation(s): 2  Gene Names: TM_0076 EC: 3.2.1.37
UniProt
Find proteins for Q9WXT1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXT1  Go to UniProtKB:  Q9WXT1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	C [auth X]	3		N/A
Glycosylation Resources
GlyTouCan:  G87429QT GlyCosmos:  G87429QT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	D [auth C]	4		N/A
Glycosylation Resources
GlyTouCan:  G60650FG GlyCosmos:  G60650FG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	E [auth A], F [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900117	C [auth X]	4beta-beta-xylotriose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.189 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.180 (DCC) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.35	α = 90
b = 100.89	β = 90
c = 179.11	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: 2024-01-24 
Deposition Author(s): Gloster, T.M., Foltanyi, F.

---

Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release