4HKG | pdb_00004hkg

Crystal Structure of Free-Standing Peptidyl Carrier Protein from Uncharacterized Acinetobacter baumannii Secondary Metabolic Pathway

• PDB DOI: https://doi.org/10.2210/pdb4HKG/pdb

• Classification: PHOSPHOPANTETHEINE BINDING PROTEIN
• Organism(s): Acinetobacter baumannii AB307-0294
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-15 Released: 2013-10-30 
• Deposition Author(s): Allen, C.L., Gulick, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Structural and bioinformatic characterization of an Acinetobacter baumannii type II carrier protein.

Allen, C.L., Gulick, A.M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1718-1725

• PubMed: 24914982 
• DOI: https://doi.org/10.1107/S1399004714008311
• Primary Citation Related Structures: 
  4HKG


• PubMed Abstract: 
  

  Microorganisms produce a variety of natural products via secondary metabolic biosynthetic pathways. Two of these types of synthetic systems, the nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), use large modular enzymes containing multiple catalytic domains in a single protein. These multidomain enzymes use an integrated carrier protein domain to transport the growing, covalently bound natural product to the neighboring catalytic domains for each step in the synthesis. Interestingly, some PKS and NRPS clusters contain free-standing domains that interact intermolecularly with other proteins. Being expressed outside the architecture of a multi-domain protein, these so-called type II proteins present challenges to understand the precise role they play. Additional structures of individual and multi-domain components of the NRPS enzymes will therefore provide a better understanding of the features that govern the domain interactions in these interesting enzyme systems. The high-resolution crystal structure of a free-standing carrier protein from Acinetobacter baumannii that belongs to a larger NRPS-containing operon, encoded by the ABBFA_003406-ABBFA_003399 genes of A. baumannii strain AB307-0294, that has been implicated in A. baumannii motility, quorum sensing and biofilm formation, is presented here. Comparison with the closest structural homologs of other carrier proteins identifies the requirements for a conserved glycine residue and additional important sequence and structural requirements within the regions that interact with partner proteins.

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Organizational Affiliation: 
• Hauptman-Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, Buffalo, NY 14203, USA.

Biological Assembly 1  

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

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

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: 20.11 kDa 
• Atom Count: 1,648 
• Modeled Residue Count: 160 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine attachment site family protein	A, B	88	Acinetobacter baumannii AB307-0294	Mutation(s): 0  Gene Names: ABBFA_003404

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	C [auth A], E [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
PEG	F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.811	α = 90
b = 61.811	β = 90
c = 76.848	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-30 
Deposition Author(s): Allen, C.L., Gulick, A.M.

Revision History  

• Version 1.0: 2013-10-30
  Type: Initial release
  
• Version 1.1: 2014-01-15
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Database references
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description