6AMZ | pdb_00006amz

Crystal structure of a domain swapped 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb6AMZ/pdb

• Classification: TRANSFERASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-11 Released: 2017-08-23 
• Deposition Author(s): Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a domain swapped 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Acinetobacter baumannii

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

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: 30.77 kDa 
• Atom Count: 2,123 
• Modelled Residue Count: 256 
• Deposited Residue Count: 281 
• 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	281	Acinetobacter baumannii	Mutation(s): 0  Gene Names: dapD EC: 2.3.1.117
UniProt
Find proteins for Q5DL43 (Acinetobacter baumannii) Explore Q5DL43  Go to UniProtKB:  Q5DL43

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	B [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36AMZ

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.25	α = 90
b = 92.25	β = 90
c = 218.44	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-23 
Deposition Author(s): Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-08-23
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description