7DZ5

Crystal structures of D-allulose 3-epimerase with D-sorbose from Sinorhizobium fredii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Substantial Improvement of an Epimerase for the Synthesis of D-Allulose by Biosensor-Based High-Throughput Microdroplet Screening

Li, C.Gao, X.Qi, H.Zhang, W.Li, L.Wei, C.Wei, M.Sun, X.Wang, S.Wang, L.Ji, Y.Mao, S.Zhu, Z.Tanokura, M.Lu, F.Qin, H.M.

(2023) Angew Chem Int Ed Engl 


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-tagatose 3-epimerase
A, B, C, D
283Sinorhizobium fredii CCBAU 83666Mutation(s): 0 
Gene Names: SF83666_b55120
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HVC (Subject of Investigation/LOI)
Query on HVC

Download Ideal Coordinates CCD File 
F [auth A],
K [auth C],
M [auth D]
alpha-D-Sorbopyranose
C6 H12 O6
LKDRXBCSQODPBY-MOJAZDJTSA-N
SDD (Subject of Investigation/LOI)
Query on SDD

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
N [auth D]
D-sorbose
C6 H12 O6
BJHIKXHVCXFQLS-PYWDMBMJSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
L [auth C],
O [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.143α = 90
b = 87.934β = 99.579
c = 128.928γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description