24FM | pdb_000024fm

Dextran glucosidase SmDG E236S in complex with isomaltose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.232 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Biochemical characterization of general acid/base glutamate mutants E236Q/S of dextran glucosidase and structural insights into trisaccharide-specificity and O-glycoligase activity

Saburi, W.Okuyama, M.Ose, T.Yao, M.Mori, H.

(2026) Biologia (Bratisl) 81: 183

Macromolecule Content 

  • Total Structure Weight: 253.62 kDa 
  • Atom Count: 18,509 
  • Modeled Residue Count: 2,144 
  • Deposited Residue Count: 2,172 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glucan 1,6-alpha-glucosidase
A, B, C, D
543Streptococcus mutansMutation(s): 1 
Gene Names: dexBSMU_883
EC: 3.2.1.70
UniProt
Find proteins for Q99040 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159))
Explore Q99040 
Go to UniProtKB:  Q99040
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99040
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose
E, F, G, H
2N/A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.869α = 90
b = 73.064β = 101.58
c = 135.081γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-23
    Type: Initial release