6LE3 | pdb_00006le3

Crystal structure of gluconate 5-dehydrogenase from Lentibacter algarum

• PDB DOI: https://doi.org/10.2210/pdb6LE3/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Lentibacter algarum
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

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

• PubMed: 32356525 
• DOI: https://doi.org/10.1107/S2053230X20005336
• Primary Citation 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 = 55.42, 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.

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Organizational Affiliation: 
• School of Life Sciences, Jilin University, Changchun, Jilin 130012, People's Republic of China.
School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510641, People's Republic of China.

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: 108.89 kDa 
• Atom Count: 7,535 
• Modeled Residue Count: 990 
• Deposited Residue Count: 1,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gluconate 5-dehydrogenase	A [auth E], B [auth F], C [auth G], D [auth H]	263	Lentibacter algarum	Mutation(s): 0  Gene Names: SAMN05444486_10810
UniProt
Find proteins for A0A1H3NGY9 (Lentibacter algarum) Explore A0A1H3NGY9  Go to UniProtKB:  A0A1H3NGY9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACE	E, F, G [auth F], H [auth F], I [auth F], J [auth G], K [auth G], L [auth G], M [auth H]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.424	α = 100.509
b = 55.484	β = 105.662
c = 79.158	γ = 97.988

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description