6FME | pdb_00006fme

Structure of sucrose phosphorylase from Bifidobacterium adolescentis bound to glycosylated resveratrol

• PDB DOI: https://doi.org/10.2210/pdb6FME/pdb

• Classification: TRANSFERASE
• Organism(s): Bifidobacterium adolescentis ATCC 15703
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-01-31 Released: 2019-03-13 
• Deposition Author(s): Grimm, C., Kraus, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 
  0.188 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Structure of sucrose phosphorylase from Bifidobacterium adolescentis bound to glycosylated resveratrol

Grimm, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 113.2 kDa 
• Atom Count: 9,200 
• Modeled Residue Count: 1,011 
• Deposited Residue Count: 1,012 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose phosphorylase	A [auth B], B [auth A]	506	Bifidobacterium adolescentis ATCC 15703	Mutation(s): 1  Gene Names: sucP, spl, BAD_0078 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
GOL	C [auth B], D [auth B], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free:  0.188 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.01	α = 90
b = 101.925	β = 90
c = 152.569	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Grimm, C., Kraus, M.

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references