2GDV

Sucrose phosphorylase from BIFIDOBACTERIUM ADOLESCENTIS reacted with sucrose

• PDB DOI: https://doi.org/10.2210/pdb2GDV/pdb

• Classification: TRANSFERASE
• Organism(s): Bifidobacterium adolescentis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-03-17 Released: 2006-09-26 
• Deposition Author(s): Skov, L.K., Mirza, O., Gajhede, M., Katsrup, J.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Structural rearrangements of Sucrose Phosphorylase from Bifidobacterium adolescentis during sucrose conversion

Mirza, O., Skov, L.K., Sprogoe, D., Van den Broek, L.A.M., Voragen, A.G.J., Katsrup, J.S., Gajhede, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 112.87 kDa 
• Atom Count: 8,959 
• Modelled Residue Count: 1,008 
• Deposited Residue Count: 1,008 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sucrose phosphorylase	A, B	504	Bifidobacterium adolescentis	Mutation(s): 0  EC: 2.4.1.7
UniProt
Find proteins for A0ZZH6 (Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)) Explore A0ZZH6  Go to UniProtKB:  A0ZZH6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	C [auth A], D [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.74	α = 90
b = 103.07	β = 90
c = 150.69	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-26 
Deposition Author(s): Skov, L.K., Mirza, O., Gajhede, M., Katsrup, J.S.

Revision History  

• Version 1.0: 2006-09-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary