3GBT | pdb_00003gbt

Crystal structure of gluconate kinase from Lactobacillus acidophilus

• PDB DOI: https://doi.org/10.2210/pdb3GBT/pdb

• Classification: TRANSFERASE
• Organism(s): Lactobacillus acidophilus NCFM
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-20 Released: 2009-03-10 
• Deposition Author(s): Zhang, Z., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.231 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

The crystal structure of gluconate kinase from Lactobacillus acidophilus

Zhang, Z., Swaminathan, S., Burley, S.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.13 kDa 
• Atom Count: 3,932 
• Modeled Residue Count: 492 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gluconate kinase	A	504	Lactobacillus acidophilus NCFM	Mutation(s): 0  Gene Names: LBA0354 EC: 2.7.1.12
UniProt
Find proteins for Q5FM28 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)) Explore Q5FM28  Go to UniProtKB:  Q5FM28

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.231 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.638	α = 90
b = 96.008	β = 93.32
c = 72.94	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Zhang, Z., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary