7ZEQ | pdb_00007zeq

Apo crystal structure of beta-xylosidase from Thermotoga maritima

PDB DOI: https://doi.org/10.2210/pdb7ZEQ/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-03-31 Released: 2023-04-19
Deposition Author(s): Gloster, T.M., Foltanyi, F.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.226 (Depositor), 0.226 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7ZEQ

This is version 1.1 of the entry. See complete history.

Literature

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

Gloster, T.M., Foltanyi, F., Hobbs, E.M., Pritchard, L.

To be published.

Macromolecule Content

Total Structure Weight: 179.69 kDa
Atom Count: 11,961
Modeled Residue Count: 1,513
Deposited Residue Count: 1,602
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylosidase	A [auth X], B [auth Y]	801	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: Tmari_0073 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

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 C [auth X] SDF format, chain D [auth Y] MOL2 format, chain C [auth X] MOL2 format, chain D [auth Y] mmCIF format, chain C [auth X] mmCIF format, chain D [auth Y]	C [auth X], D [auth Y]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth X] Focus chain D [auth Y] Interactions & Density Focus chain C [auth X] Focus chain D [auth Y]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.226 (Depositor), 0.226 (DCC)
R-Value Work: 0.194 (Depositor), 0.194 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.08	α = 90
b = 98.59	β = 90
c = 100.92	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2023-04-19
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.