8B81 | pdb_00008b81

The structure of Gan1D W433A in complex with cellobiose-6-phosphate

• PDB DOI: https://doi.org/10.2210/pdb8B81/pdb

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


• Deposited: 2022-10-04 Released: 2022-10-19 
• Deposition Author(s): Snyder, J., Lansky, S., Zehavi, A., Shoham, Y., Shoham, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

The structure of Gan1D W433A in complex with cellobiose-6-phosphate

Snyder, J., Lansky, S., Zehavi, A., 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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 111.43 kDa 
• Atom Count: 8,977 
• Modeled Residue Count: 948 
• Deposited Residue Count: 956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 6-phospho-beta-galactobiosidase	A, B	478	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	C [auth E], D	2		N/A
Glycosylation Resources
GlyTouCan:  G15380AW GlyCosmos:  G15380AW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	E [auth A], F [auth A], G [auth A], H [auth A]	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	C [auth D], D [auth E]	beta-cellobiose-6-phosphate	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.9	α = 90
b = 68.38	β = 99.36
c = 149.8	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-19 
Deposition Author(s): Snyder, J., Lansky, S., Zehavi, A., Shoham, Y., Shoham, G.

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Funding Organization	Location	Grant Number
Not funded	Israel	--

Revision History  

• Version 1.0: 2022-10-19
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description