1J1N

Structure Analysis of AlgQ2, A Macromolecule(Alginate)-Binding Periplasmic Protein Of Sphingomonas Sp. A1., Complexed with an Alginate Tetrasaccharide

• PDB DOI: https://doi.org/10.2210/pdb1J1N/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Sphingomonas sp. A1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-12-11 Released: 2003-06-10 
• Deposition Author(s): Momma, K., Mikami, B., Mishima, Y., Hashimoto, W., Murata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.214 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 116.03 kDa 
• Atom Count: 9,046 
• Modelled Residue Count: 984 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AlgQ2	A, B	492	Sphingomonas sp. A1	Mutation(s): 0
UniProt
Find proteins for Q9KWT5 (Sphingomonas sp) Explore Q9KWT5  Go to UniProtKB:  Q9KWT5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid	C, D	4		N/A
Glycosylation Resources
GlyTouCan:  G97659EB GlyCosmos:  G97659EB

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.214 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.63	α = 90
b = 53.881	β = 107.53
c = 114.924	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-10 
Deposition Author(s): Momma, K., Mikami, B., Mishima, Y., Hashimoto, W., Murata, K.

Revision History  

• Version 1.0: 2003-06-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary