3MI6 | pdb_00003mi6

Crystal structure of the alpha-galactosidase from Lactobacillus brevis, Northeast Structural Genomics Consortium Target LbR11.

• PDB DOI: https://doi.org/10.2210/pdb3MI6/pdb

• Classification: HYDROLASE
• Organism(s): Levilactobacillus brevis ATCC 367
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-09 Released: 2010-04-28 
• Deposition Author(s): Vorobiev, S., Chen, Y., Seetharaman, J., Belote, R., Sahdev, S., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.241 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of the alpha-galactosidase from Lactobacillus brevis.

Vorobiev, S., Chen, Y., Seetharaman, J., Belote, R., Sahdev, S., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 347.04 kDa 
• Atom Count: 24,417 
• Modeled Residue Count: 2,958 
• Deposited Residue Count: 2,980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-galactosidase	A, B, C, D	745	Levilactobacillus brevis ATCC 367	Mutation(s): 0  Gene Names: LVIS_1758 EC: 3.2.1.22
UniProt
Find proteins for Q03PP7 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947)) Explore Q03PP7  Go to UniProtKB:  Q03PP7

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.241 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.938	α = 90
b = 158.818	β = 90
c = 166.017	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXDE	phasing
PHENIX	refinement
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-28 
Deposition Author(s): Vorobiev, S., Chen, Y., Seetharaman, J., Belote, R., Sahdev, S., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary