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), 0.188 (DCC)
R-Value Work:
0.164 (Depositor), 0.164 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

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

Gloster, T.M., Foltanyi, F.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WXT1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G60650FG GlyCosmos: G60650FG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.189 (Depositor), 0.188 (DCC)
R-Value Work: 0.164 (Depositor), 0.164 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.