8YAI | pdb_00008yai

Crystal structure of glucose 1-dehydrogenase mutant1 from Limosilactobacillus fermentum

• PDB DOI: https://doi.org/10.2210/pdb8YAI/pdb

• Classification: HYDROLASE
• Organism(s): Limosilactobacillus fermentum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-02-09 Released: 2024-10-30 
• Deposition Author(s): Cong, L., Wang, J.J., Wei, H.L., Liu, W.D., You, S.
• Funding Organization(s): Chinese Scholarship Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure-Guided Engineering of a Short-Chain Dehydrogenase LfSDR1 for Efficient Biosynthesis of (R)-9-(2-Hydroxypropyl)adenine, the Key Intermediate of Tenofovir

Wang, Q., Cong, L., Guo, J., Wang, J., Han, X., Zhang, W., Liu, W., Wei, H., You, S.

(2024) Adv Synth Catal 

• DOI: https://doi.org/10.1002/adsc.202400752

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 105.28 kDa 
• Atom Count: 7,231 
• Modeled Residue Count: 928 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SDR family oxidoreductase	A, B, C [auth D], D [auth C]	247	Limosilactobacillus fermentum	Mutation(s): 4  Gene Names: GC247_10055 EC: 1.1.1.163 (UniProt), 1.1.1.53 (UniProt), 1.1.1.51 (UniProt), 1.1.1.47 (UniProt)
UniProt
Find proteins for A0A1D7ZZ64 (Limosilactobacillus fermentum) Explore A0A1D7ZZ64  Go to UniProtKB:  A0A1D7ZZ64

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.205	α = 90
b = 104.514	β = 110.96
c = 72.331	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Cong, L., Wang, J.J., Wei, H.L., Liu, W.D., You, S.

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Funding Organization	Location	Grant Number
Chinese Scholarship Council	China	--

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description