6NU8 | pdb_00006nu8

Structure of sucrose-6-phosphate hydrolase from Lactobacillus gasseri in complex with fructose

• PDB DOI: https://doi.org/10.2210/pdb6NU8/pdb

• Classification: HYDROLASE
• Organism(s): Lactobacillus gasseri 224-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-31 Released: 2020-02-05 
• Deposition Author(s): Lima, M.Z.T., Muniz, J.R.C.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.165 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Literature

Structure of sucrose-6-phosphate hydrolase from Lactobacillus gasseri in complex with fructose

Lima, M.Z.T., Muniz, J.R.C.

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 and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 55.84 kDa 
• Atom Count: 4,468 
• Modeled Residue Count: 488 
• Deposited Residue Count: 489 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose-6-phosphate hydrolase	A	489	Lactobacillus gasseri 224-1	Mutation(s): 0  Gene Names: HMPREF9209_2365 EC: 3.2.1.26
UniProt
Find proteins for D1YK18 (Lactobacillus gasseri 224-1) Explore D1YK18  Go to UniProtKB:  D1YK18

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FRU	B [auth A]	beta-D-fructofuranose C6 H12 O6 RFSUNEUAIZKAJO-ARQDHWQXSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.165 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.86	α = 90
b = 103.86	β = 90
c = 102	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
TRUNCATE	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-05 
Deposition Author(s): Lima, M.Z.T., Muniz, J.R.C.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2017/16291-5
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	309767/2015-6
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	486546/2013-6
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	308865/2018-9

Revision History  

• Version 1.0: 2020-02-05
  Type: Initial release
  
• Version 1.1: 2020-02-12
  Changes: Structure summary
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Structure summary