7BLH | pdb_00007blh

Structure of CBM BT3015C from Bacteroides thetaiotaomicron in complex with O-GalNAc core 1-Thr

PDB DOI: https://doi.org/10.2210/pdb7BLH/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-01-18 Released: 2022-03-02
Deposition Author(s): Costa, R.L., Carvalho, A.L.
Funding Organization(s): Foundation for Science and Technology (FCT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.203 (Depositor), 0.203 (DCC)
R-Value Work:
0.157 (Depositor), 0.160 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7BLH

Ligand Structure Quality Assessment

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

Literature

Structural basis for mucin-type O-glycan recognition by proteins of a Bacteroides thetaiotaomicron polysaccharide utilization loci

Costa, R.L., Correia, V.G.

To be published.

Macromolecule Content

Total Structure Weight: 18.46 kDa
Atom Count: 1,373
Modeled Residue Count: 142
Deposited Residue Count: 162
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
family 32 carbohydrate-binding module from Bacteroides thetaiotaomicron	A [auth AAAA]	162	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_3015
UniProt
Find proteins for Q8A3D9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A3D9 Go to UniProtKB: Q8A3D9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A3D9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	B [auth C]	2		O-Glycosylation	Interactions Focus chain B [auth C] Interactions & Density Focus chain B [auth C]
Glycosylation Resources
GlyTouCan: G00031MO GlyCosmos: G00031MO GlyGen: G00031MO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THR (Subject of Investigation/LOI) Query on THR Download:Ideal Coordinates CCD File SDF format, chain C [auth AAAA] MOL2 format, chain C [auth AAAA] mmCIF format, chain C [auth AAAA]	C [auth AAAA]	THREONINE C₄ H₉ N O₃ AYFVYJQAPQTCCC-GBXIJSLDSA-N		Interactions Focus chain C [auth AAAA] Interactions & Density Focus chain C [auth AAAA]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth AAAA] MOL2 format, chain D [auth AAAA] mmCIF format, chain D [auth AAAA]	D [auth AAAA]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth AAAA] Interactions & Density Focus chain D [auth AAAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.203 (Depositor), 0.203 (DCC)
R-Value Work: 0.157 (Depositor), 0.160 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.525	α = 90
b = 64.011	β = 90
c = 70.211	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
SADABS	data reduction
SAINT	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Foundation for Science and Technology (FCT)	Portugal	PTDC/BIA-MIB/31730/2017

Revision History (Full details and data files)

Version 1.0: 2022-03-02
Type: Initial release
Version 1.1: 2024-01-31
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.