7O0E | pdb_00007o0e

Crystal structure of GH30 (mutant E188A) complexed with aldotriuronic acid from Thermothelomyces thermophila.

PDB DOI: https://doi.org/10.2210/pdb7O0E/pdb

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

Deposited: 2021-03-26 Released: 2021-09-08
Deposition Author(s): Dimarogona, M., Kosinas, C., Feiler, C., Weiss, M.S., Topakas, E., Nikolaivits, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.191 (Depositor), 0.200 (DCC)
R-Value Work:
0.155 (Depositor), 0.167 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 98.88 kDa
Atom Count: 7,645
Modeled Residue Count: 893
Deposited Residue Count: 904
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 G], B [auth A]	452	Thermothelomyces thermophilus ATCC 42464	Mutation(s): 1 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: 1	Glycosylation Focus chain B [auth A]
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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	4		N-Glycosylation	Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	D, E	3		N/A	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G78055TN GlyCosmos: G78055TN

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain F [auth G] SDF format, chain G SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth G] MOL2 format, chain F [auth G] MOL2 format, chain G MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth G] mmCIF format, chain F [auth G] mmCIF format, chain G mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth G]	F [auth G], G, J [auth G], K [auth A], L [auth A]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain F [auth G] Focus chain G Focus chain J [auth G] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain F [auth G] Focus chain G Focus chain J [auth G] Focus chain K [auth A] Focus chain L [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth G] SDF format, chain I [auth G] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain H [auth G] MOL2 format, chain I [auth G] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain H [auth G] mmCIF format, chain I [auth G] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	H [auth G], I [auth G], M [auth A], N [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth G] Focus chain I [auth G] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain H [auth G] Focus chain I [auth G] Focus chain M [auth A] Focus chain N [auth A]