8QME

Structural characterization of beta-xyloxidase XynB2 from Geobacillus stearothermophilus CECT43

PDB DOI: https://doi.org/10.2210/pdb8QME/pdb

Classification: HYDROLASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-09-22 Released: 2024-03-27
Deposition Author(s): Gavira, J.A., Martinez-Rodriguez, S.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.213
R-Value Work: 0.178
R-Value Observed: 0.179

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural Characterization of beta-Xylosidase XynB2 from Geobacillus stearothermophilus CECT43: A Member of the Glycoside Hydrolase Family GH52

Gavira, J.A., Contreras, L.M., Alshamaa, H.M., Clemente-Jimenez, J.M., Rodriguez-Vico, F., Las Heras-Vazquez, F.J., Martinez-Rodriguez, S.

(2024) Crystals (Basel) 14

DOI: https://doi.org/10.3390/cryst14010018

Macromolecule Content

Total Structure Weight: 325.74 kDa
Atom Count: 23,817
Modelled Residue Count: 2,729
Deposited Residue Count: 2,844
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylosidase	A, B, C, D	711	Geobacillus stearothermophilus	Mutation(s): 3 Gene Names: GA8_03270
UniProt
Find proteins for A0A7U9HVH2 (Geobacillus sp. A8) Explore A0A7U9HVH2 Go to UniProtKB: A0A7U9HVH2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7U9HVH2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth D] EA [auth D] FA [auth D] GA [auth D] H [auth A] AA [auth D], EA [auth D], FA [auth D], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], K [auth A], Q [auth B], R [auth B], S [auth B], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	BA [auth D] DA [auth D] E [auth A] F [auth A] G [auth A] BA [auth D], DA [auth D], E [auth A], F [auth A], G [auth A], M [auth B], N [auth B], P [auth B], T [auth C], U [auth C], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	CA [auth D], L [auth A], O [auth B], W [auth C], X [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth D] Focus chain L [auth A] Focus chain O [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain L [auth A] Focus chain O [auth B] Focus chain W [auth C] Focus chain X [auth C]