9CX5 | pdb_00009cx5

Acinetobacter baumannii BamA POTRAs 1-4, space group P3221

• PDB DOI: https://doi.org/10.2210/pdb9CX5/pdb

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


• Deposited: 2024-07-30 Released: 2024-10-30 
• Deposition Author(s): Overly Cottom, C., Noinaj, N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.237 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

Structural characterization of the POTRA domains from A. baumannii reveals new conformations in BamA.

Cottom, C.O., Stephenson, R., Ricci, D., Yang, L., Gumbart, J.C., Noinaj, N.

(2024) Structure 32: 2038

• PubMed: 39293443 
• DOI: https://doi.org/10.1016/j.str.2024.08.013
• Primary Citation of Related Structures:  
  9CX4, 9CX5


• PubMed Abstract: 
  

  Recent studies have demonstrated BamA, the central component of the β-barrel assembly machinery (BAM), as an important therapeutic target to combat infections caused by Acinetobacter baumannii and other Gram-negative pathogens. Homology modeling indicates BamA in A. baumannii consists of five polypeptide transport-associated (POTRA) domains and a β-barrel membrane domain. We characterized the POTRA domains of BamA from A. baumannii in solution using size-exclusion chromatography small angle X-ray scattering (SEC-SAXS) analysis and determined crystal structures in two conformational states that are drastically different than those previously observed in BamA from other bacteria, indicating that the POTRA domains are even more conformationally dynamic than has been observed previously. Molecular dynamics simulations of the POTRA domains from A. baumannii and Escherichia coli allowed us to identify key structural features that contribute to the observed novel states. Together, these studies expand on our current understanding of the conformational plasticity within BamA across differing bacterial species.

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Organizational Affiliation: 
• Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
Achaogen, Inc., South San Francisco, CA, USA.
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA; School of Physics, Georgia Institute of Technology, Atlanta, GA, USA.
Department of Biological Sciences, Purdue University, West Lafayette, IN, USA; Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA; Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 75.21 kDa 
• Atom Count: 5,167 
• Modeled Residue Count: 656 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamA	A, B	330	Acinetobacter baumannii	Mutation(s): 0  Gene Names: yaeT, bamA, ATCC19606_15070
UniProt
Find proteins for A0A7U4DDM8 (Acinetobacter baumannii (strain ACICU)) Explore A0A7U4DDM8  Go to UniProtKB:  A0A7U4DDM8

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.237 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.917	α = 90
b = 94.917	β = 90
c = 220.297	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Overly Cottom, C., Noinaj, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM127884
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM127896
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01AI127793

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Database references