5U25 | pdb_00005u25

Crystal structure of a dihydrolipoyl dehydrogenase from Neisseria gonorrhoeae bound to FAD

• PDB DOI: https://doi.org/10.2210/pdb5U25/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Neisseria gonorrhoeae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-29 Released: 2016-12-21 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.209 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.169 (Depositor) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a dihydrolipoyl dehydrogenase from Neisseria gonorrhoeae bound to FAD

Edwards, T.E., Horanyi, P.S., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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)

Macromolecule Content 

• Total Structure Weight: 64.32 kDa 
• Atom Count: 3,752 
• Modeled Residue Count: 478 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoamide dehydrogenase (E3 component of pyruvate and 2-oxoglutarate dehydrogenase complexes)	A	602	Neisseria gonorrhoeae	Mutation(s): 0  Gene Names:  lpdA, WHOF_00599C, WHOF_01471, WHOG_01174, WHOG_01559, WHON_01176, WHON_01441, WHOO_01105, WHOO_01298, WHOW_00549, NGK_1362 EC: 1.8.1.4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.209 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.169 (Depositor) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.66	α = 90
b = 142.66	β = 90
c = 70.39	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary