3IMH

CRYSTAL STRUCTURE OF GALACTOSE 1-EPIMERASE FROM Lactobacillus acidophilus NCFM

• PDB DOI: https://doi.org/10.2210/pdb3IMH/pdb

• Classification: ISOMERASE
• Organism(s): Lactobacillus acidophilus NCFM
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-08-10 Released: 2009-08-18 
• Deposition Author(s): Patskovsky, Y., Toro, R., Dickey, M., Chang, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.170 
• R-Value Work: 0.140 
• R-Value Observed: 0.141 

Literature

CRYSTAL STRUCTURE OF GALACTOSE 1-EPIMERASE FROM Lactobacillus acidophilus

Patskovsky, Y., Toro, R., Dickey, M., Chang, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 77.05 kDa 
• Atom Count: 6,441 
• Modelled Residue Count: 664 
• Deposited Residue Count: 676 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose-1-epimerase	A, B	338	Lactobacillus acidophilus NCFM	Mutation(s): 1  Gene Names: galM, LBA1457 EC: 5.1.3.3
UniProt
Find proteins for Q5FJ46 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)) Explore Q5FJ46  Go to UniProtKB:  Q5FJ46

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], G [auth A], H [auth A], I [auth A], K [auth A], M [auth B], N [auth B], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A], J [auth A], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.170 
• R-Value Work: 0.140 
• R-Value Observed: 0.141 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.683	α = 90
b = 134.683	β = 90
c = 103.027	γ = 90

Software Package:

Software Name	Purpose
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Patskovsky, Y., Toro, R., Dickey, M., Chang, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-13
  Changes: Database references
• Version 1.6: 2024-02-21
  Changes: Data collection