5OKE

Conservatively refined structure of Gan1D-E170Q, a catalytic mutant of a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with cellobiose-6-phosphate

• PDB DOI: https://doi.org/10.2210/pdb5OKE/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-07-25 Released: 2017-10-18 
• Deposition Author(s): Lansky, S., Zehavi, A., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 0.155 
• R-Value Work: 0.133 
• R-Value Observed: 0.133 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

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)

Macromolecule Content

• Total Structure Weight: 227.51 kDa 
• Atom Count: 18,080 
• Modelled Residue Count: 1,847 
• Deposited Residue Count: 1,940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 6-phospho-beta-galactobiosidase	A, B, C, D	485	Geobacillus stearothermophilus	Mutation(s): 1  Gene Names: gan1D EC: 3.2.1.85
UniProt
Find proteins for W8QF82 (Geobacillus stearothermophilus) Explore W8QF82  Go to UniProtKB:  W8QF82

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
6-O-phosphono-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	E, F	2		N/A
Glycosylation Resources
GlyTouCan:  G15380AW GlyCosmos:  G15380AW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BG6	G [auth A], N [auth B]	6-O-phosphono-beta-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-VFUOTHLCSA-N
GOL	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], V [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	M [auth A], U [auth C], W [auth D]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900053	E, F	beta-cellobiose-6-phosphate	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 0.155 
• R-Value Work: 0.133 
• R-Value Observed: 0.133 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.599	α = 90
b = 97.48	β = 97.66
c = 105.269	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Lansky, S., Zehavi, A., Shoham, Y., Shoham, G.

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references
• Version 1.2: 2017-11-01
  Changes: Database references
• Version 1.3: 2017-11-29
  Changes: Database references
• Version 1.4: 2017-12-06
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary