6KPB | pdb_00006kpb

The crystal structure of the JACKDAW/IDD10 bound to the homodimeric SCL3

PDB DOI: https://doi.org/10.2210/pdb6KPB/pdb

Classification: TRANSCRIPTION
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-08-15 Released: 2020-09-02
Deposition Author(s): Hirano, Y., Hakoshima, T.
Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.214 (Depositor), 0.224 (DCC)
R-Value Work:
0.191 (Depositor), 0.198 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6KPB

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

Literature

Structure of the SCL3 homodimer bound to the BIRD/IDD transcription factor

Hirano, Y., Shimizu, R., Nishimura, T., Morita, M.T., Hakoshima, T.

To be published.

Macromolecule Content

Total Structure Weight: 56.17 kDa
Atom Count: 3,067
Modeled Residue Count: 392
Deposited Residue Count: 501
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Scarecrow-like protein 3	A [auth C]	484	Arabidopsis thaliana	Mutation(s): 0 Gene Names: SCL3, At1g50420, F11F12.22
UniProt
Find proteins for Q9LPR8 (Arabidopsis thaliana) Explore Q9LPR8 Go to UniProtKB: Q9LPR8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LPR8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Zinc finger protein JACKDAW	B	17	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q700D2 (Arabidopsis thaliana) Explore Q700D2 Go to UniProtKB: Q700D2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q700D2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C MOL2 format, chain C mmCIF format, chain C	C	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.214 (Depositor), 0.224 (DCC)
R-Value Work: 0.191 (Depositor), 0.198 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.037	α = 90
b = 112.037	β = 90
c = 70.979	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR14M5
Japan Society for the Promotion of Science	Japan	17K07448

Revision History (Full details and data files)

Version 1.0: 2020-09-02
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.