8P1R | pdb_00008p1r

Bifidobacterium asteroides alpha-L-fucosidase (TT1819) catalytic mutant.

PDB DOI: https://doi.org/10.2210/pdb8P1R/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Bifidobacterium asteroides
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-05-12 Released: 2024-03-27
Deposition Author(s): Owen, C.D., Penner, M., Gascuena, A.N., Wu, H., Hernando, P.J., Monaco, S., Le Gall, G., Gardner, R., Ndeh, D., Urbanowicz, P.A., Spencer, D.I.R., Walsh, M.A., Angulo, J., Juge, N.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Spanish Ministry of Science, Innovation, and Universities, H2020 Marie Curie Actions of the European Commission, UK Research and Innovation (UKRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.188 (Depositor), 0.197 (DCC)
R-Value Work:
0.160 (Depositor), 0.172 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Exploring sequence, structure and function of microbial fucosidases from glycoside hydrolase GH29 family

Owen, C.D., Penner, M., Gascuena, A.N., Wu, H., Hernando, P.J., Monaco, S., Le Gall, G., Gardner, R., Ndeh, D., Urbanowicz, P.A., Spencer, D.I.R., Walsh, M.A., Angulo, J., Juge, N.

To be published.

Macromolecule Content

Total Structure Weight: 238.68 kDa
Atom Count: 18,342
Modeled Residue Count: 2,005
Deposited Residue Count: 2,100
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifidobacterium asteroides alpha-L-fucosidase (TT1819) catalytic mutant	A, B, C, D, E A, B, C, D, E, F	350	Bifidobacterium asteroides	Mutation(s): 0
UniProt
Find proteins for A0A0F4KU40 (Bifidobacterium asteroides) Explore A0A0F4KU40 Go to UniProtKB: A0A0F4KU40
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0F4KU40
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth B] G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], N [auth D], O [auth E], P [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Q [auth F] MOL2 format, chain Q [auth F] mmCIF format, chain Q [auth F]	Q [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth F] Interactions & Density Focus chain Q [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.188 (Depositor), 0.197 (DCC)
R-Value Work: 0.160 (Depositor), 0.172 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.684	α = 90
b = 136.252	β = 90
c = 160.451	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/P010660/1
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2019-109395GB-I00
H2020 Marie Curie Actions of the European Commission	European Union	814102
UK Research and Innovation (UKRI)	United Kingdom	BB/M029042/