6BNG

Structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb6BNG/pdb

• Classification: TRANSFERASE
• Organism(s): Acinetobacter baumannii AB307-0294
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-11-16 Released: 2017-12-20 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.226 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Acinetobacter baumannii

Abendroth, J., Delker, S.L., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 64.71 kDa 
• Atom Count: 4,319 
• Modelled Residue Count: 547 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxyphosphooctonate aldolase	A, B	289	Acinetobacter baumannii AB307-0294	Mutation(s): 0  Gene Names: kdsA, ABBFA_001556 EC: 2.5.1.55
UniProt
Find proteins for B7H226 (Acinetobacter baumannii (strain AB307-0294)) Explore B7H226  Go to UniProtKB:  B7H226

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.226 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.69	α = 90
b = 83.93	β = 90
c = 87.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description