5CK1 | pdb_00005ck1

selenomethionine BT4246

• PDB DOI: https://doi.org/10.2210/pdb5CK1/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.9 kDa 
• Atom Count: 5,585 
• Modeled Residue Count: 584 
• Deposited Residue Count: 641 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SusD homolog	A	641	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.792	α = 90
b = 115.738	β = 90
c = 116.656	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Koropatkin, N.M.

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

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary