6EX6 | pdb_00006ex6

The GH127, Beta-arabinofuranosidase, BT3674

PDB DOI: https://doi.org/10.2210/pdb6EX6/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-11-07 Released: 2018-11-21
Deposition Author(s): Munoz-Munoz, J., Gilbert, H.J.
Funding Organization(s): European Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.221 (Depositor), 0.227 (DCC)
R-Value Work:
0.176 (Depositor), 0.188 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The cellular location of endo-acting galactanases confers keystone or recipient status to arabinogalactan degrading organisms of the human gut microbiota

Munoz-Munoz, J., Cartmell, A., Ndeh, D., Lowe, E.C., Briggs, J., Basle, A., Terrapon, N., Stott, K., Dupree, P., Fernnandes, P.Z., Shah, S., Williams, S.J., Labourel, A., Henrissat, B., Gilbert, H.J.

To be published.

Macromolecule Content

Total Structure Weight: 146.25 kDa
Atom Count: 10,524
Modeled Residue Count: 1,267
Deposited Residue Count: 1,296
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Six-hairpin glycosidase	A [auth B], B [auth A]	648	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_3674
UniProt
Find proteins for Q8A1I7 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A1I7 Go to UniProtKB: Q8A1I7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A1I7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth A]	C [auth B], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.221 (Depositor), 0.227 (DCC)
R-Value Work: 0.176 (Depositor), 0.188 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.821	α = 90
b = 136.821	β = 90
c = 135.582	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Munoz-Munoz, J.

Funding Organization	Location	Grant Number
European Research Council	United Kingdom	322820

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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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.