7AX5 | pdb_00007ax5

Anammox-specific acyl carrier protein from Kuenenia stuttgartiensis; ensemble refinement

• PDB DOI: https://doi.org/10.2210/pdb7AX5/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Candidatus Kuenenia stuttgartensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-11-09 Released: 2021-08-11 
• Deposition Author(s): Dietl, A., Barends, T.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.234 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Dynamics in an unusual acyl carrier protein from a ladderane lipid-synthesizing organism.

Dietl, A., Barends, T.R.M.

(2022) Proteins 90: 73-82

• PubMed: 34310758 
• DOI: https://doi.org/10.1002/prot.26187
• Primary Citation Related Structures: 
  7AUF, 7AX5


• PubMed Abstract: 
  

  Anaerobic ammonium-oxidizing (anammox) bacteria express a distinct acyl carrier protein implicated in the biosynthesis of the highly unusual "ladderane" lipids these organisms produce. This "anammox-specific" ACP, or amxACP, shows several unique features such as a conserved FF motif and an unusual sequence in the functionally important helix III. Investigation of the protein's structure and dynamics, both in the crystal by ensemble refinement and by MD simulations, reveals that helix III adopts a rare six-residue-long 3 ₁₀ -helical conformation that confers a large degree of conformational and positional variability on this part of the protein. This way of introducing structural flexibility by using the inherent properties of 3 ₁₀ -helices appears unique among ACPs. Moreover, the structure suggests a role for the FF motif in shielding the thioester linkage between the protein's prosthetic group and its acyl cargo from hydrolysis.

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Organizational Affiliation: 
• Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany.

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: light scattering

Macromolecule Content 

• Total Structure Weight: 11.19 kDa 
• Atom Count: 724 
• Modeled Residue Count: 89 
• Deposited Residue Count: 94 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Similar to acyl carrier protein	A	94	Candidatus Kuenenia stuttgartensis	Mutation(s): 0  Gene Names: acpP, acpP_2, KSMBR1_3472, kuste3603
UniProt
Find proteins for Q1Q2X6 (Kuenenia stuttgartiensis) Explore Q1Q2X6  Go to UniProtKB:  Q1Q2X6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.234 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.81	α = 90
b = 76.81	β = 90
c = 30.9	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-08-11 
Deposition Author(s): Dietl, A., Barends, T.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	724362

Revision History  

• Version 1.0: 2021-08-11
  Type: Initial release
  
• Version 1.1: 2021-12-22
  Changes: Database references
• Version 1.2: 2024-06-19
  Changes: Data collection