6NOB | pdb_00006nob

Structure of Glycoside Hydrolase family 32 from Bifidobacterium adolescentis

• PDB DOI: https://doi.org/10.2210/pdb6NOB/pdb

• Classification: HYDROLASE
• Organism(s): Bifidobacterium adolescentis ATCC 15703
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-16 Released: 2020-01-22 
• Deposition Author(s): Mera, A.M., 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: 2.44 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structure of GH32 from Bifidobacterium adolescentis

Mera, A., Lima, M.Z.T., Bernardes, A., Garcia, W., Muniz, J.R.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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.79 kDa 
• Atom Count: 5,342 
• Modeled Residue Count: 634 
• Deposited Residue Count: 637 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-fructofuranosidase	A	637	Bifidobacterium adolescentis ATCC 15703	Mutation(s): 0  Gene Names: BAD_1325 EC: 3.2.1.26
UniProt
Find proteins for A1A323 (Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)) Explore A1A323  Go to UniProtKB:  A1A323

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth A], G [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.903	α = 90
b = 130.903	β = 90
c = 132.937	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
TRUNCATE	data reduction
Aimless	data scaling
DIALS	data collection
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Mera, A.M., 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	486546/2013-6
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	309767/2015-6

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description