6XA5

Trehalose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain

• PDB DOI: https://doi.org/10.2210/pdb6XA5/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Marinomonas primoryensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-03 Released: 2021-06-02 
• Deposition Author(s): Guo, S., Davies, P.L.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 0.131 
• R-Value Work: 0.118 
• R-Value Observed: 0.119 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 20.7 kDa 
• Atom Count: 1,762 
• Modelled Residue Count: 187 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antifreeze protein	A	188	Marinomonas primoryensis	Mutation(s): 0
UniProt
Find proteins for A1YIY3 (Marinomonas primoryensis) Explore A1YIY3  Go to UniProtKB:  A1YIY3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G92130SN GlyCosmos:  G92130SN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	B	trehalose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 0.131 
• R-Value Work: 0.118 
• R-Value Observed: 0.119 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.27	α = 90
b = 50.64	β = 90
c = 79.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-02 
Deposition Author(s): Guo, S., Davies, P.L.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)		--

Revision History  

• Version 1.0: 2021-06-02
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description