6WQM

Crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from Bartonella henselae

• PDB DOI: https://doi.org/10.2210/pdb6WQM/pdb

• Classification: TRANSFERASE
• Organism(s): Bartonella henselae str. Houston-1
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-04-29 Released: 2020-05-13 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.253 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

Crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from Bartonella henselae

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 191.43 kDa 
• Atom Count: 13,232 
• Modelled Residue Count: 1,681 
• Deposited Residue Count: 1,734 
• 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, D, E, F	289	Bartonella henselae str. Houston-1	Mutation(s): 0  Gene Names: dapD, BH00720 EC: 2.3.1.117
UniProt
Find proteins for Q6G549 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / CCUG 30454 / Houston 1)) Explore Q6G549  Go to UniProtKB:  Q6G549

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	G [auth A], H [auth A], I [auth A], J [auth B], K [auth D], L [auth D], M [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.253 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m36wqm

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.84	α = 90
b = 228.22	β = 120.1
c = 71.19	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description