6ZNW | pdb_00006znw

Methanosaeta concilii ATP citrate lyase (D541A mutant) in complex with (3S)-citryl-CoA.

• PDB DOI: https://doi.org/10.2210/pdb6ZNW/pdb

• Classification: LYASE
• Organism(s): Methanothrix soehngenii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-07-06 Released: 2021-07-14 
• Deposition Author(s): Verschueren, K.H.G., Verstraete, K.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.203 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase.

Verstraete, K., Verschueren, K.H.G., Dansercoer, A., Savvides, S.N.

(2021) Nat Struct Mol Biol 28: 636-638

• PubMed: 34294920 
• DOI: https://doi.org/10.1038/s41594-021-00624-3
• Primary Citation Related Structures: 
  6Z2H, 6ZNW

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Organizational Affiliation: 
• VIB-UGent Center for Inflammation Research, Ghent, Belgium. [e-mail].
Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium. [e-mail].
VIB-UGent Center for Inflammation Research, Ghent, Belgium.
Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
VIB-UGent Center for Inflammation Research, Ghent, Belgium. [e-mail].
Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

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

Macromolecule Content 

• Total Structure Weight: 117.71 kDa 
• Atom Count: 8,289 
• Modeled Residue Count: 1,018 
• Deposited Residue Count: 1,052 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate lyase, subunit 1	A	421	Methanothrix soehngenii	Mutation(s): 0  Gene Names: ACLY-A EC: 2.3.3.8
UniProt
Find proteins for A0A7K4AG75 (Methanothrix soehngenii) Explore A0A7K4AG75  Go to UniProtKB:  A0A7K4AG75

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methanosaeta concilii ACLY-B	B	631	Methanothrix soehngenii	Mutation(s): 0  Gene Names: ACLY-B EC: 2.3.3.8
UniProt
Find proteins for A0A7K4AGC1 (Methanothrix soehngenii) Explore A0A7K4AGC1  Go to UniProtKB:  A0A7K4AGC1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q5B (Subject of Investigation/LOI)	F [auth B]	(3S)-citryl-Coenzyme A C27 H42 N7 O22 P3 S IHVFHZGGMJDGGZ-VPXVXCNZSA-N
FLC (Subject of Investigation/LOI)	C [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
PO4 (Subject of Investigation/LOI)	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.203 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.531	α = 90
b = 154.373	β = 90
c = 276.054	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Verschueren, K.H.G., Verstraete, K.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G0G0619N

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2021-08-11
  Changes: Database references
• Version 1.2: 2021-08-25
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description