9O8Y | pdb_00009o8y

Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (DapD) from Bordetella pertussis (succinyl-CoA bound)

• PDB DOI: https://doi.org/10.2210/pdb9O8Y/pdb

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


• Deposited: 2025-04-17 Released: 2025-04-30 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.182 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (dapD) from Bordetella pertussis (succinyl-CoA bound)

Ung, A.R., Lovell, S., Cooper, A., Battaile, K.P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 90.95 kDa 
• Atom Count: 6,597 
• Modeled Residue Count: 778 
• Deposited Residue Count: 834 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase	A, B, C	278	Bordetella pertussis Tohama I	Mutation(s): 0  Gene Names: dapD, BP1764 EC: 2.3.1.117
UniProt
Find proteins for P0A4U8 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore P0A4U8  Go to UniProtKB:  P0A4U8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SCA (Subject of Investigation/LOI)	F [auth A]	SUCCINYL-COENZYME A C25 H40 N7 O19 P3 S VNOYUJKHFWYWIR-ITIYDSSPSA-N
CL	D [auth A], E [auth A], G [auth B], H [auth B], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.182 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39O8Y

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.264	α = 90
b = 88.645	β = 90
c = 117.291	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release