4ZZE

Raffinose and panose binding protein from Bifidobacterium animalis subsp. lactis Bl-04, bound with panose

• PDB DOI: https://doi.org/10.2210/pdb4ZZE/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bifidobacterium animalis subsp. lactis Bl-04
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-22 Released: 2016-06-29 
• Deposition Author(s): Fredslund, F., Ejby, M., Andersen, J.M., Slotboom, D.J., Hachem, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.205 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

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: 89.8 kDa 
• Atom Count: 7,099 
• Modelled Residue Count: 753 
• Deposited Residue Count: 792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar binding protein of ABC transporter system	A, B	396	Bifidobacterium animalis subsp. lactis Bl-04	Mutation(s): 0  Gene Names: Balac_1599
UniProt
Find proteins for A0A1A9TAB8 (Bifidobacterium animalis subsp. lactis (strain Bl-04 / DGCC2908 / RB 4825 / SD5219)) Explore A0A1A9TAB8  Go to UniProtKB:  A0A1A9TAB8

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan:  G05704WW GlyCosmos:  G05704WW GlyGen:  G05704WW

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	J [auth A], K [auth A], P [auth B], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.205 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.88	α = 90
b = 91.33	β = 90
c = 142.05	γ = 90

Software Package:

Software Name	Purpose
xia2	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-29 
Deposition Author(s): Fredslund, F., Ejby, M., Andersen, J.M., Slotboom, D.J., Hachem, M.A.

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary