5CJZ | pdb_00005cjz

BT4246 with galactose

PDB DOI: https://doi.org/10.2210/pdb5CJZ/pdb

Classification: mucin-binding protein
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-15 Released: 2016-10-12
Deposition Author(s): Koropatkin, N.M.
Funding Organization(s): University of Michigan Host Microbiome Initiative

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.211 (Depositor), 0.212 (DCC)
R-Value Work:
0.175 (Depositor), 0.179 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Mechanistic insight into mucin degradation by the human gut microbiota reveals targeting of the glycoprotein core

Ndeh, D.A., Nakjang, S., Kwiatkowski, K.J., Koropatkin, N.M., Hirt, R.P., Bolam, D.N.

To be published.

Macromolecule Content

Total Structure Weight: 72.26 kDa
Atom Count: 5,811
Modeled Residue Count: 603
Deposited Residue Count: 626
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SusD homolog	A	626	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_4246
UniProt
Find proteins for Q89ZX5 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89ZX5 Go to UniProtKB: Q89ZX5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q89ZX5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GAL Query on GAL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CS Query on CS Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A], G [auth A]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.211 (Depositor), 0.212 (DCC)
R-Value Work: 0.175 (Depositor), 0.179 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.925	α = 90
b = 155.925	β = 90
c = 114.315	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-10-12

Deposition Author(s):

Koropatkin, N.M.

Funding Organization	Location	Grant Number
University of Michigan Host Microbiome Initiative	United States	--

Revision History (Full details and data files)

Version 1.0: 2016-10-12
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary

5CJZ | pdb_00005cjz

BT4246 with galactose

Literature

Mechanistic insight into mucin degradation by the human gut microbiota reveals targeting of the glycoprotein core

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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