5C3M | pdb_00005c3m

Crystal structure of Gan4C, a GH4 6-phospho-glucosidase from Geobacillus stearothermophilus

• PDB DOI: https://doi.org/10.2210/pdb5C3M/pdb

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


• Deposited: 2015-06-17 Released: 2016-06-29 
• Deposition Author(s): Cohen, T., Lansky, S., Zehavi, A., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free: 
  0.306 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Gan4C, a GH4 6-phospho-glucosidase from Geobacillus stearothermophilus

Cohen, T., Lansky, S., Zehavi, A., Shoham, Y., Shoham, G.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (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: Dihedral - D2  (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: 197.51 kDa 
• Atom Count: 12,494 
• Modeled Residue Count: 1,640 
• Deposited Residue Count: 1,788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 6-phospho-beta-glucosidase	A, B, C, D	447	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: gan4C EC: 3.2.1.86
UniProt
Find proteins for W8R9V4 (Geobacillus stearothermophilus) Explore W8R9V4  Go to UniProtKB:  W8R9V4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	E [auth A], F [auth B], G [auth C], H [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free:  0.306 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.324	α = 90
b = 83.198	β = 113.61
c = 151.372	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description