7VMA | pdb_00007vma

The X-ray crystallographic structure of amylo-alpha-1,6-glucosidase from Thermococcus gammatolerans STB12

• PDB DOI: https://doi.org/10.2210/pdb7VMA/pdb

• Classification: HYDROLASE
• Organism(s): Thermococcus gammatolerans EJ3
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-10-08 Released: 2022-10-12 
• Deposition Author(s): Li, Z.F., Ban, X.F., Wang, Y.M., Li, C.M., Gu, Z.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.328 (Depositor), 0.330 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: in silico

Literature

The X-ray Crystallographic Structure of Amylo-alpha-1,6-glucosidase from Thermococcus gannatilerans STB12

Li, Z.F., Ban, X.F., Wang, Y.M., Li, C.M., Gu, Z.B.

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)

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: 137.41 kDa 
• Atom Count: 9,718 
• Modeled Residue Count: 1,240 
• Deposited Residue Count: 1,240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amylo-alpha-1,6-glucosidase, putative archaeal type glycogen debranching enzyme (Gde)	A, B	620	Thermococcus gammatolerans EJ3	Mutation(s): 0  Gene Names: gde, TGAM_1568 EC: 3.2.1.33
UniProt
Find proteins for C5A758 (Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3)) Explore C5A758  Go to UniProtKB:  C5A758

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.328 (Depositor), 0.330 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.087	α = 90
b = 108.087	β = 90
c = 225.199	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Li, Z.F., Ban, X.F., Wang, Y.M., Li, C.M., Gu, Z.B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31722040
National Natural Science Foundation of China (NSFC)	China	31771935
National Natural Science Foundation of China (NSFC)	China	31901628

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description