6AON

1.72 Angstrom Resolution Crystal Structure of 2-Oxoglutarate Dehydrogenase Complex Subunit Dihydrolipoamide Dehydrogenase from Bordetella pertussis in Complex with FAD

• PDB DOI: https://doi.org/10.2210/pdb6AON/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bordetella pertussis Tohama I
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-08-16 Released: 2017-08-23 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., McChesney, C., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.205 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

1.72 Angstrom Resolution Crystal Structure of 2-Oxoglutarate Dehydrogenase Complex Subunit Dihydrolipoamide Dehydrogenase from Bordetella pertussis in Complex with FAD

Minasov, G., Wawrzak, Z., Skarina, T., McChesney, C., Grimshaw, S., Savchenko, A., Anderson, W.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 102.48 kDa 
• Atom Count: 8,521 
• Modelled Residue Count: 946 
• Deposited Residue Count: 956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase	A, B	478	Bordetella pertussis Tohama I	Mutation(s): 0  Gene Names: odhL, BP1126 EC: 1.8.1.4
UniProt
Find proteins for Q7VZ16 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VZ16  Go to UniProtKB:  Q7VZ16

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.205 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 4₁
• Diffraction Data: https://doi.org/10.18430/m36aon

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.801	α = 90
b = 68.801	β = 90
c = 199.396	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-23 
Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., McChesney, C., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2017-08-23
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Database references, Structure summary
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description