4GBJ | pdb_00004gbj

Crystal structure of NAD-binding 6-phosphogluconate dehydrogenase from Dyadobacter fermentans

• PDB DOI: https://doi.org/10.2210/pdb4GBJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Dyadobacter fermentans DSM 18053
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-27 Released: 2012-09-05 
• Deposition Author(s): Michalska, K., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Crystal structure of NAD-binding 6-phosphogluconate dehydrogenase from Dyadobacter fermentans

Michalska, K., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 128.77 kDa 
• Atom Count: 9,154 
• Modeled Residue Count: 1,158 
• Deposited Residue Count: 1,188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase NAD-binding	A, B, C, D	297	Dyadobacter fermentans DSM 18053	Mutation(s): 0  Gene Names: Dfer_3638
UniProt
Find proteins for C6VV20 (Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / CIP 107007 / KCTC 52180 / NS114)) Explore C6VV20  Go to UniProtKB:  C6VV20

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth B], F [auth C], G [auth C], H [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34GBJ

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.633	α = 90
b = 89.645	β = 90
c = 151.506	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
BUCCANEER	model building
Coot	model building
BUSTER	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
BUCCANEER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Michalska, K., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary