6INZ

Crystal structure of solute-binding protein complexed with unsaturated hyaluronan disaccharide

• PDB DOI: https://doi.org/10.2210/pdb6INZ/pdb

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


• Deposited: 2018-10-29 Released: 2019-09-11 
• Deposition Author(s): Oiki, S., Mikami, B., Murata, K., Hashimoto, W.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.217 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

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

Macromolecule Content

• Total Structure Weight: 58.72 kDa 
• Atom Count: 4,232 
• Modelled Residue Count: 474 
• Deposited Residue Count: 505 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular solute-binding protein family 1	A	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-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G14110BE GlyCosmos:  G14110BE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.217 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.74	α = 90
b = 97.501	β = 90
c = 132.443	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
MOLREP	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	--

Revision History  

• Version 1.0: 2019-09-11
  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