4NZJ

Crystal structure of a putative alpha-galactosidase (BF1418) from Bacteroides fragilis NCTC 9343 at 1.57 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb4NZJ/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-12 Released: 2013-12-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.169 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Literature

Crystal structure of a putative alpha-galactosidase (BF1418) from Bacteroides fragilis NCTC 9343 at 1.57 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.97 kDa 
• Atom Count: 4,357 
• Modelled Residue Count: 468 
• Deposited Residue Count: 477 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative alpha-galactosidase	A	477	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF9343_1347, YP_211072.1, agaA_2, NCTC9343_02997 EC: 3.2.1.22

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.169 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 4₂ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M34NZJ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.614	α = 90
b = 114.614	β = 90
c = 77.051	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations