5U95 | pdb_00005u95

Structure of the open conformation of 4-coumarate-CoA ligase from Nicotiana tabacum

• PDB DOI: https://doi.org/10.2210/pdb5U95/pdb

• Classification: LIGASE
• Organism(s): Nicotiana tabacum
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2016-12-15 Released: 2017-03-22 
• Deposition Author(s): Morioka, W.P., Bianchetti, C.M.
• Funding Organization(s): University of Wisconsin Oshkosh The Oshkosh Student Scholarship and Creative Activity Program

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Structure of the open conformation of 4-coumarate-CoA ligase from Nicotiana tabacum

Morioka, W.P., Bianchetti, C.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 238.1 kDa 
• Atom Count: 15,622 
• Modelled Residue Count: 1,975 
• Deposited Residue Count: 2,168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-coumarate--CoA ligase 2	A, B, C, D	542	Nicotiana tabacum	Mutation(s): 0  Gene Names: 4CL2 EC: 6.2.1.12 (PDB Primary Data), 6.2.1.34 (UniProt), 6.2.1 (UniProt)
UniProt
Find proteins for O24146 (Nicotiana tabacum) Explore O24146  Go to UniProtKB:  O24146

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth A], G [auth B], H [auth C], I [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.259	α = 90
b = 108.259	β = 90
c = 183.22	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Morioka, W.P., Bianchetti, C.M.

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Funding Organization	Location	Grant Number
University of Wisconsin Oshkosh The Oshkosh Student Scholarship and Creative Activity Program	United States	--

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description