7NCX | pdb_00007ncx

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free:
0.158 (Depositor), 0.144 (DCC)
R-Value Work:
0.122 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G2Q1N4
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth AAA]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain B [auth BBB] Interactions & Density Focus chain B [auth BBB]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth AAA] MOL2 format, chain G [auth AAA] mmCIF format, chain G [auth AAA]	G [auth AAA]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth AAA] Interactions & Density Focus chain G [auth AAA]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain D [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Interactions & Density Focus chain D [auth AAA]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA]	E [auth AAA], F [auth AAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free: 0.158 (Depositor), 0.144 (DCC)
R-Value Work: 0.122 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-09-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-09-08
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary