6LE3

Crystal structure of gluconate 5-dehydrogenase from Lentibacter algarum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of gluconate 5-dehydrogenase from Lentibacter algarum.

Tian, D.Fu, X.Cao, W.Yuan, H.

(2020) Acta Crystallogr F Struct Biol Commun 76: 228-234

  • DOI: 10.1107/S2053230X20005336
  • Primary Citation of Related Structures:  
    6LE3

  • PubMed Abstract: 
  • Gluconate 5-dehydrogenase (Ga5DH; EC 1.1.1.69) from Lentibacter algarum (LaGa5DH) was recombinantly expressed in Escherichia coli and purified to homogeneity. The protein was crystallized and the crystal structure was solved at 2.1 Å resolution. The crystal belonged to the monoclinic system, with space group P1 and unit-cell parameters a = 55 ...

    Gluconate 5-dehydrogenase (Ga5DH; EC 1.1.1.69) from Lentibacter algarum (LaGa5DH) was recombinantly expressed in Escherichia coli and purified to homogeneity. The protein was crystallized and the crystal structure was solved at 2.1 Å resolution. The crystal belonged to the monoclinic system, with space group P1 and unit-cell parameters a = 55.42, b = 55.48, c = 79.16 Å, α = 100.51, β = 105.66, γ = 97.99°. The structure revealed LaGaDH to be a tetramer, with each subunit consisting of six α-helices and three antiparallel β-hairpins. LaGa5DH has high structural similarity to other Ga5DH proteins, demonstrating that this enzyme is highly conserved.


    Organizational Affiliation

    School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510641, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gluconate 5-dehydrogenaseA [auth E], B [auth F], C [auth G], D [auth H]263Lentibacter algarumMutation(s): 0 
Gene Names: SAMN05444486_10810
UniProt
Find proteins for A0A1H3NGY9 (Lentibacter algarum)
Explore A0A1H3NGY9 
Go to UniProtKB:  A0A1H3NGY9
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.424α = 100.509
b = 55.484β = 105.662
c = 79.158γ = 97.988
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2019-11-23 
  • Released Date: 2020-05-13 
  • Deposition Author(s): Yuan, H.

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release