4ZEP | pdb_00004zep

Structure of Gan1D, a 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with 6-phospho-glucose

• PDB DOI: https://doi.org/10.2210/pdb4ZEP/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-04-20 Released: 2016-06-29 
• Deposition Author(s): Lansky, S., Zehavi, A., Dvir, H., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Structure of Gan1D, a 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with 6-phospho-glucose

Lansky, S., Zehavi, A., Dvir, H., Shoham, Y., Shoham, G.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 113.38 kDa 
• Atom Count: 8,365 
• Modeled Residue Count: 948 
• Deposited Residue Count: 970 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 6-phospho-beta-galactobiosidase	A, B	485	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: gan1D EC: 3.2.1.85
UniProt
Find proteins for W8QF82 (Geobacillus stearothermophilus) Explore W8QF82  Go to UniProtKB:  W8QF82

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BG6	C [auth A], G [auth B]	6-O-phosphono-beta-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-VFUOTHLCSA-N
GOL	D [auth A], E [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	F [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.158	α = 90
b = 68.944	β = 100.39
c = 152.896	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-29 
Deposition Author(s): Lansky, S., Zehavi, A., Dvir, H., Shoham, Y., Shoham, G.

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary