3WFA | pdb_00003wfa

Catalytic role of the calcium ion in GH97 inverting glycoside hydrolase

• PDB DOI: https://doi.org/10.2210/pdb3WFA/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-18 Released: 2014-07-16 
• Deposition Author(s): Okuyama, M., Yoshida, T., Hondoh, H., Mori, H., Yao, M., Kimura, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Catalytic role of the calcium ion in GH97 inverting glycoside hydrolase

Okuyama, M., Yoshida, T., Hondoh, H., Mori, H., Yao, M., Kimura, A.

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: 167.27 kDa 
• Atom Count: 12,548 
• Modeled Residue Count: 1,403 
• Deposited Residue Count: 1,452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-glucosidase	A, B	726	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: susB EC: 3.2.1.3
UniProt
Find proteins for G8JZS4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore G8JZS4  Go to UniProtKB:  G8JZS4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDT	D [auth A], F [auth B]	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C10 H16 N2 O8 KCXVZYZYPLLWCC-UHFFFAOYSA-N
NA	C [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.52	α = 90
b = 111.96	β = 100.49
c = 102.36	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-16 
Deposition Author(s): Okuyama, M., Yoshida, T., Hondoh, H., Mori, H., Yao, M., Kimura, A.

Revision History  

• Version 1.0: 2014-07-16
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description