7NCX

Crystal structure of GH30 (double mutant EE) from Thermothelomyces thermophila.

• PDB DOI: https://doi.org/10.2210/pdb7NCX/pdb

• Classification: HYDROLASE
• Organism(s): Thermothelomyces thermophilus ATCC 42464
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2021-01-29 Released: 2021-09-08 
• Deposition Author(s): Dimarogona, M., Nikolaivits, E., Topakas, E., Weiss, M., Feiler, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.158 
• R-Value Work: 0.122 

Starting Model: experimental

Literature

Unique features of the bifunctional GH30 from Thermothelomyces thermophila revealed by structural and mutational studies

Nikolaivits, E., Pentari, C., Kosinas, C., Feiler, C.G., Spiliopoulou, M., Weiss, M.S., Dimarogona, M., Topakas, E.

(2021) Carbohydrate Polymers 273: 118553

• DOI: https://doi.org/10.1016/j.carbpol.2021.118553

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 53.35 kDa 
• Atom Count: 4,082 
• Modelled Residue Count: 443 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH30 family xylanase	A [auth AAA]	482	Thermothelomyces thermophilus ATCC 42464	Mutation(s): 2  Gene Names: Xyn30A, MYCTH_38558 EC: 3.2.1
UniProt
Find proteins for G2Q1N4 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799)) Explore G2Q1N4  Go to UniProtKB:  G2Q1N4
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B [auth BBB]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC GlyCosmos:  G09724ZC GlyGen:  G09724ZC

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth AAA]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG	D [auth AAA]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth AAA]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth AAA], F [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.158 
• R-Value Work: 0.122 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.887	α = 90
b = 87.315	β = 90
c = 107.917	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-08 
Deposition Author(s): Dimarogona, M., Nikolaivits, E., Topakas, E., Weiss, M., Feiler, C.G.

Revision History  

• Version 1.0: 2021-09-08
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description