7EKU | pdb_00007eku

Crystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (W958A)

• PDB DOI: https://doi.org/10.2210/pdb7EKU/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Nakaseomyces glabratus CBS 138
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-04-06 Released: 2022-04-13 
• Deposition Author(s): Shen, M., Xiang, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (W958A)

Shen, M., Xiang, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 350.86 kDa 
• Atom Count: 24,309 
• Modeled Residue Count: 3,023 
• Deposited Residue Count: 3,072 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-alpha-glucanotransferase	A, B	1,536	Nakaseomyces glabratus CBS 138	Mutation(s): 1  Gene Names: GDB1 EC: 2.4.1.25 (PDB Primary Data), 3.2.1.33 (PDB Primary Data)
UniProt
Find proteins for Q6FSK0 (Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138)) Explore Q6FSK0  Go to UniProtKB:  Q6FSK0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.221	α = 90
b = 200.651	β = 90
c = 259.976	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-13 
Deposition Author(s): Shen, M., Xiang, S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870769
National Natural Science Foundation of China (NSFC)	China	32071205

Revision History  

• Version 1.0: 2022-04-13
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description