6ZNW | pdb_00006znw

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.203 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q5BClick on this verticalbar to view detailsBest fitted FLCClick on this verticalbar to view detailsBest fitted PO4Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history. 


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


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Citrate lyase, subunit 1421Methanothrix soehngeniiMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7K4AG75
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Methanosaeta concilii ACLY-B631Methanothrix soehngeniiMutation(s): 0 
Gene Names: ACLY-B
EC: 2.3.3.8
UniProt
Find proteins for A0A7K4AGC1 (Methanothrix soehngenii)
Explore A0A7K4AGC1 
Go to UniProtKB:  A0A7K4AGC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7K4AGC1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.203 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.531α = 90
b = 154.373β = 90
c = 276.054γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q5BClick on this verticalbar to view detailsBest fitted FLCClick on this verticalbar to view detailsBest fitted PO4Click on this verticalbar to view details

View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumG0G0619N

Revision History  (Full details and data files)

  • 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