4BZH | pdb_00004bzh

Crystal structure of galactose mutarotase GalM from Bacillus subtilis in complex with maltose and trehalose

• PDB DOI: https://doi.org/10.2210/pdb4BZH/pdb

• Classification: ISOMERASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2013-07-25 Released: 2014-08-13 
• Deposition Author(s): Vanden Broeck, A., Sauvage, E., Herman, R., Kerff, F., Duez, C., Charlier, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.269 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Galactose Mutarotase Galm from Bacillus Subtilis in Complex with Maltose and Trehalose

Vanden Broeck, A., Sauvage, E., Herman, R., Kerff, F., Duez, C., Charlier, P.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 76.03 kDa 
• Atom Count: 5,591 
• Modeled Residue Count: 645 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALDOSE 1-EPIMERASE	A, B	324	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: GALM EC: 5.1.3.3
UniProt
Find proteins for P39840 (Bacillus subtilis (strain 168)) Explore P39840  Go to UniProtKB:  P39840

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	C, E	2		N/A
Glycosylation Resources
GlyTouCan: G92130SN GlyCosmos: G92130SN

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	D, F	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	I [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	C, E	trehalose	Oligosaccharide / Nutrient

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	D, F	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.269 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.194	α = 90
b = 83.291	β = 90
c = 124.754	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-13 
Deposition Author(s): Vanden Broeck, A., Sauvage, E., Herman, R., Kerff, F., Duez, C., Charlier, P.

Revision History  

• Version 1.0: 2014-08-13
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary