5XS8

Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with two sulfate groups at C-4 and C-6 positions of GalNAc

• PDB DOI: https://doi.org/10.2210/pdb5XS8/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Streptobacillus moniliformis DSM 12112
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-06-12 Released: 2018-01-17 
• Deposition Author(s): Oiki, S., Kamochi, R., Mikami, B., Murata, K., Hashimoto, W.
• Funding Organization(s): Grants-in-Aids for Scientific Research from the Japanese Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.215 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 232.45 kDa 
• Atom Count: 16,765 
• Modelled Residue Count: 1,896 
• Deposited Residue Count: 2,020 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular solute-binding protein family 1	A, B, C, D	505	Streptobacillus moniliformis DSM 12112	Mutation(s): 0  Gene Names: Smon_0123
UniProt
Find proteins for D1AWE0 (Streptobacillus moniliformis (strain ATCC 14647 / DSM 12112 / NCTC 10651 / 9901)) Explore D1AWE0  Go to UniProtKB:  D1AWE0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4,6-di-O-sulfo-beta-D-galactopyranose	E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G26418LS GlyCosmos:  G26418LS

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	I [auth A], J [auth B], K [auth C], L [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.215 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.741	α = 89.99
b = 69.208	β = 90.04
c = 165.967	γ = 90.03

Software Package:

Software Name	Purpose
PHENIX	refinement
MOLREP	model building
HKL-2000	data processing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Oiki, S., Kamochi, R., Mikami, B., Murata, K., Hashimoto, W.

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Funding Organization	Location	Grant Number
Grants-in-Aids for Scientific Research from the Japanese Society for the Promotion of Science	Japan	--

Revision History  

• Version 1.0: 2018-01-17
  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: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary