8WEV | pdb_00008wev

Crystal structure of Feruoyl-CoA Synthetase complexed with AMP from Amycolatopsis thermoflava

• PDB DOI: https://doi.org/10.2210/pdb8WEV/pdb

• Classification: LIGASE
• Organism(s): Amycolatopsis thermoflava N1165
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-09-18 Released: 2024-09-25 
• Deposition Author(s): Seok, J., Kim, K.-J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of feruloyl-CoA synthetase from Amycolatopsis thermoflava.

Seok, J., Kim, K.-J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 104.95 kDa 
• Atom Count: 7,342 
• Modeled Residue Count: 962 
• Deposited Residue Count: 982 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Feruloyl-CoA Synthetase	A, B	491	Amycolatopsis thermoflava N1165	Mutation(s): 0  Gene Names: EDD35_5915 EC: 6.2.1.34
UniProt
Find proteins for Q9EY88 (Amycolatopsis sp) Explore Q9EY88  Go to UniProtKB:  Q9EY88

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	C [auth A], G [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.764	α = 90
b = 132.1	β = 90
c = 161.995	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Seok, J., Kim, K.-J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release