3A09 | pdb_00003a09

Crystal structure of Sphingomonas sp. A1 alginate-binding protein AlgQ1 in complex with unsaturated trimannuronate

• PDB DOI: https://doi.org/10.2210/pdb3A09/pdb

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


• Deposited: 2009-03-12 Released: 2010-03-16 
• Deposition Author(s): Itoh, T., Mikami, B., Hashimoto, W., Murata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.208 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.133 (DCC) 
• R-Value Observed: 
  0.131 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Sphingomonas sp. A1 alginate-binding protein AlgQ1 in complex with unsaturated trimannuronate

Itoh, T., Mikami, B., Hashimoto, W., Murata, K.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 57.5 kDa 
• Atom Count: 4,950 
• Modeled Residue Count: 490 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AlgQ1	A	490	Sphingomonas sp. A1	Mutation(s): 0  Gene Names: algQ1
UniProt
Find proteins for A0ACD6B942 (Sphingomonas sp) Explore A0ACD6B942  Go to UniProtKB:  A0ACD6B942

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid	B	3		N/A
Glycosylation Resources
GlyTouCan: G91327GF GlyCosmos: G91327GF

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.208 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.133 (DCC) 
• R-Value Observed: 0.131 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.378	α = 90
b = 67.725	β = 94.98
c = 63.206	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Itoh, T., Mikami, B., Hashimoto, W., Murata, K.

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary