4ATF

Crystal structure of inactivated mutant beta-agarase B in complex with agaro-octaose

• PDB DOI: https://doi.org/10.2210/pdb4ATF/pdb

• Classification: HYDROLASE
• Organism(s): Zobellia galactanivorans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-05-06 Released: 2012-07-25 
• Deposition Author(s): Bernard, T., Hehemann, J.H., Correc, G., Jam, M., Michel, G., Czjzek, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.190 
• R-Value Work: 0.134 
• R-Value Observed: 0.137 

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 148.04 kDa 
• Atom Count: 11,129 
• Modelled Residue Count: 1,185 
• Deposited Residue Count: 1,232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-AGARASE B	A, B, C, D	308	Zobellia galactanivorans	Mutation(s): 1  EC: 3.2.1.81
UniProt
Find proteins for Q9RGX8 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij)) Explore Q9RGX8  Go to UniProtKB:  Q9RGX8

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-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose	E, F, G, H	8		N/A
Glycosylation Resources
GlyTouCan:  G63389KU GlyCosmos:  G63389KU

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	I [auth A], J [auth B], K [auth C], L [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.190 
• R-Value Work: 0.134 
• R-Value Observed: 0.137 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.187	α = 90
b = 106.234	β = 93.22
c = 96.983	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-25 
Deposition Author(s): Bernard, T., Hehemann, J.H., Correc, G., Jam, M., Michel, G., Czjzek, M.

Revision History  

• Version 1.0: 2012-07-25
  Type: Initial release
  
• Version 1.1: 2012-09-12
  Changes: Database references, Structure summary
• Version 1.2: 2017-08-09
  Changes: Data collection
• 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: Data collection, Database references, Refinement description, Structure summary