5U95

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.260
R-Value Work: 0.193
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

Morioka, W.P., Bianchetti, C.M.

To be published.

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

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(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for O24146 (Nicotiana tabacum) Explore O24146 Go to UniProtKB: O24146
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O24146
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D]	E [auth A], F [auth A], G [auth B], H [auth C], I [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.260
R-Value Work: 0.193
R-Value Observed: 0.194
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

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Entry History & Funding Information

Deposition Data

Released Date: 2017-03-22

Deposition Author(s):

Morioka, W.P.

Bianchetti, C.M.

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

Revision History (Full details and data files)

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

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Help and Resources

5U95

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)