3ZWE

Structure of BambL, a lectin from Burkholderia ambifaria, complexed with blood group B epitope

• PDB DOI: https://doi.org/10.2210/pdb3ZWE/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Burkholderia ambifaria AMMD
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-07-29 Released: 2011-12-21 
• Deposition Author(s): Audfray, A., Claudinon, J., Abounit, S., Ruvoen-Clouet, N., Larson, G., Wimmerova, M., LePendu, J., Romer, W., Varrot, A., Imberty, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.266 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 30.28 kDa 
• Atom Count: 2,354 
• Modelled Residue Count: 261 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BAMBL LECTIN	A, B, C	87	Burkholderia ambifaria AMMD	Mutation(s): 0
UniProt
Find proteins for Q0B4G1 (Burkholderia ambifaria (strain ATCC BAA-244 / AMMD)) Explore Q0B4G1  Go to UniProtKB:  Q0B4G1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose	D	2		N/A
Glycosylation Resources
GlyTouCan:  G00068MO GlyCosmos:  G00068MO GlyGen:  G00068MO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	E, F	4		N/A
Glycosylation Resources
GlyTouCan:  G06873PC GlyCosmos:  G06873PC GlyGen:  G06873PC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUC	G [auth A], H [auth B], I [auth C]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.266 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.98	α = 90
b = 49.14	β = 90
c = 102.71	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: 2011-12-21 
Deposition Author(s): Audfray, A., Claudinon, J., Abounit, S., Ruvoen-Clouet, N., Larson, G., Wimmerova, M., LePendu, J., Romer, W., Varrot, A., Imberty, A.

Revision History  

• Version 1.0: 2011-12-21
  Type: Initial release
  
• Version 1.1: 2012-02-15
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary