6PTL

Structure of the self-association domain of the chromatin looping factor LDB1

• PDB DOI: https://doi.org/10.2210/pdb6PTL/pdb

• Classification: GENE REGULATION
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-07-16 Released: 2020-07-22 
• Deposition Author(s): Macindoe, I., Silva, A., Guss, J.M., Mackay, J.P., Matthews, J.M.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.271 
• R-Value Work: 0.245 
• R-Value Observed: 0.246 

Literature

Structure of the self-association domain of the chromatin looping factor LDB1

Macindoe, I., Silva, A., Guss, J.M., Mackay, J.P., Matthews, J.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: light scattering, SAXS, cross-linking, mass spectrometry

Macromolecule Content

• Total Structure Weight: 22.61 kDa 
• Atom Count: 1,230 
• Modelled Residue Count: 142 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIM domain-binding protein 1	A	192	Mus musculus	Mutation(s): 0  Gene Names: Ldb1, Nli
UniProt
Find proteins for P70662 (Mus musculus) Explore P70662  Go to UniProtKB:  P70662

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.271 
• R-Value Work: 0.245 
• R-Value Observed: 0.246 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.869	α = 90
b = 81.869	β = 90
c = 66.828	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): Macindoe, I., Silva, A., Guss, J.M., Mackay, J.P., Matthews, J.M.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1064442
Australian Research Council (ARC)	Australia	DP190102543

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references