8BIT

Crystal structure of acyl-CoA synthetase from Metallosphaera sedula in complex with Coenzyme A and acetyl-AMP

• PDB DOI: https://doi.org/10.2210/pdb8BIT/pdb

• Classification: LIGASE
• Organism(s): Metallosphaera sedula DSM 5348
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-11-02 Released: 2023-11-15 
• Deposition Author(s): Capra, N., Thunnissen, A.M.W.H., Janssen, D.B.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.277 
• R-Value Work: 0.210 
• R-Value Observed: 0.214 

Literature

Adapting an acyl CoA ligase from Metallosphaera sedula for lactam formation by structure-guided protein engineering

Capra, N., Lelievre, C., Toure, O., Fossey-Jouenne, A., Vergne-Vaxelaire, C., Janssen, D.B., Thunnissen, A.M.W.H., Zaparucha, A.

(2024) Front Catal 4

• DOI: https://doi.org/10.3389/fctls.2024.1360129

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 132.76 kDa 
• Atom Count: 9,185 
• Modelled Residue Count: 1,124 
• Deposited Residue Count: 1,140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxybutyrate--CoA ligase 1	A [auth B], B [auth A]	570	Metallosphaera sedula DSM 5348	Mutation(s): 0  Gene Names: Msed_0406 EC: 6.2.1.40 (PDB Primary Data), 6.2.1.1 (PDB Primary Data), 6.2.1.2 (PDB Primary Data), 6.2.1.17 (PDB Primary Data)
UniProt
Find proteins for A4YDT1 (Metallosphaera sedula (strain ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2)) Explore A4YDT1  Go to UniProtKB:  A4YDT1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA (Subject of Investigation/LOI)	D [auth B], F [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
6R9 (Subject of Investigation/LOI)	C [auth B], E [auth A]	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate C12 H16 N5 O8 P UBPVOHPZRZIJHM-WOUKDFQISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.277 
• R-Value Work: 0.210 
• R-Value Observed: 0.214 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.806	α = 90
b = 93.19	β = 91.12
c = 131.685	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-15 
Deposition Author(s): Capra, N., Thunnissen, A.M.W.H., Janssen, D.B.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-11-15
  Type: Initial release
  
• Version 2.0: 2024-02-14
  Type: Coordinate replacement
  Reason: Atomic clashes
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Structure summary
• Version 2.1: 2024-03-13
  Changes: Database references