5G49 | pdb_00005g49

Crystal structure of the Arabodopsis thaliana histone-fold dimer L1L NF-YC3

PDB DOI: https://doi.org/10.2210/pdb5G49/pdb

Classification: TRANSCRIPTION
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-05-06 Released: 2016-12-07
Deposition Author(s): Gnesutta, N., Saad, D., Chaves-Sanjuan, A., Mantovani, R., Nardini, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.200 (Depositor), 0.204 (DCC)
R-Value Work:
0.162 (Depositor), 0.167 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the Arabidopsis thaliana L1L/NF-YC3 Histone-fold Dimer Reveals Specificities of the LEC1 Family of NF-Y Subunits in Plants.

Gnesutta, N., Saad, D., Chaves-Sanjuan, A., Mantovani, R., Nardini, M.

(2017) Mol Plant 10: 645-648

PubMed: 27871811 Search on PubMed
DOI: https://doi.org/10.1016/j.molp.2016.11.006
Primary Citation Related Structures:
5G49

Organizational Affiliation

Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.

Macromolecule Content

Total Structure Weight: 22.82 kDa
Atom Count: 1,715
Modeled Residue Count: 191
Deposited Residue Count: 192
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6	A	97	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q84W66 (Arabidopsis thaliana) Explore Q84W66 Go to UniProtKB: Q84W66
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84W66
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3	B	95	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9ZVL3 (Arabidopsis thaliana) Explore Q9ZVL3 Go to UniProtKB: Q9ZVL3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZVL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	D [auth B], E [auth B], F [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.200 (Depositor), 0.204 (DCC)
R-Value Work: 0.162 (Depositor), 0.167 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.344	α = 90
b = 81.691	β = 90
c = 95.998	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-12-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-12-07
Type: Initial release
Version 1.1: 2017-03-15
Changes: Database references
Version 1.2: 2017-04-12
Changes: Database references
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description