6ER4

Ruminococcus gnavus IT-sialidase CBM40 bound to alpha2,6 sialyllactose

• PDB DOI: https://doi.org/10.2210/pdb6ER4/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Mediterraneibacter gnavus ATCC 29149
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-16 Released: 2018-05-02 
• Deposition Author(s): Owen, C.D., Tailford, L.E., Taylor, G.L., Juge, N.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.135 
• R-Value Work: 0.108 
• R-Value Observed: 0.110 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 43.75 kDa 
• Atom Count: 3,704 
• Modelled Residue Count: 383 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BNR/Asp-box repeat protein	A, B	194	Mediterraneibacter gnavus ATCC 29149	Mutation(s): 0  Gene Names: RUMGNA_02694
UniProt
Find proteins for A7B557 (Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9)) Explore A7B557  Go to UniProtKB:  A7B557

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan:  G28868ZC GlyCosmos:  G28868ZC GlyGen:  G28868ZC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	F [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
GOL	E [auth A], G [auth B], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900066	C, D	6'-sialyl-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.135 
• R-Value Work: 0.108 
• R-Value Observed: 0.110 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.74	α = 90
b = 72.2	β = 103.88
c = 51.41	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Owen, C.D., Tailford, L.E., Taylor, G.L., Juge, N.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/F016778/1

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary