4BQ4

Structural analysis of an exo-beta-agarase

• PDB DOI: https://doi.org/10.2210/pdb4BQ4/pdb

• Classification: HYDROLASE
• Organism(s): Saccharophagus degradans 2-40
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-29 Released: 2013-08-14 
• Deposition Author(s): Pluvinage, B., Hehemann, J.H., Boraston, A.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.209 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 170.75 kDa 
• Atom Count: 13,247 
• Modelled Residue Count: 1,500 
• Deposited Residue Count: 1,500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-AGARASE	A, B	750	Saccharophagus degradans 2-40	Mutation(s): 1  EC: 3.2.1.81
UniProt
Find proteins for Q21HC5 (Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)) Explore Q21HC5  Go to UniProtKB:  Q21HC5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose	C, D	4		N/A
Glycosylation Resources
GlyTouCan:  G46404PO GlyCosmos:  G46404PO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	I [auth A], J [auth A], O [auth B], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.209 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.23	α = 90
b = 116.01	β = 90
c = 208.76	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Pluvinage, B., Hehemann, J.H., Boraston, A.B.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2013-08-21
  Changes: Database references
• Version 1.2: 2013-08-28
  Changes: Atomic model, Database references, Derived calculations
• Version 1.3: 2013-10-16
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary