6KPD | pdb_00006kpd

The crystal structure of the BALDIBIS/IDD9 bound to the homodimeric SCL3

• PDB DOI: https://doi.org/10.2210/pdb6KPD/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., Shimizu, R., Hakoshima, T.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 54.68 kDa 
• Atom Count: 3,012 
• Modeled Residue Count: 390 
• Deposited Residue Count: 490 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Scarecrow-like protein 3	A [auth C]	452	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Zinc finger protein BALDIBIS	B	38	Arabidopsis thaliana	Mutation(s): 0  Gene Names: BIB, IDD9, IDZ1, At3g45260, F18N11.20
UniProt
Find proteins for Q944L3 (Arabidopsis thaliana) Explore Q944L3  Go to UniProtKB:  Q944L3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.384	α = 90
b = 103.384	β = 90
c = 68.69	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-02 
Deposition Author(s): Hirano, Y., Shimizu, R., Hakoshima, T.

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

Revision History  

• Version 1.0: 2020-09-02
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description