9BPO | pdb_00009bpo

Structure of the self-association domain of LDB2

• PDB DOI: https://doi.org/10.2210/pdb9BPO/pdb

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


• Deposited: 2024-05-08 Released: 2025-03-19 
• Deposition Author(s): Vu, T.H., Patel, K., Smith, N.C., Matthews, J.M.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.266 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: in silico

Literature

Structure of the self-association domain of LDB2

Vu, T.H., Patel, K., Smith, N.C., 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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 87.24 kDa 
• Atom Count: 5,882 
• Modeled Residue Count: 697 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIM domain-binding protein 2	A, B, C, D	184	Mus musculus	Mutation(s): 0  Gene Names: Ldb2, Clim1
UniProt
Find proteins for O55203 (Mus musculus) Explore O55203  Go to UniProtKB:  O55203

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.266 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.276	α = 90
b = 42.969	β = 101.56
c = 121.768	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Vu, T.H., Patel, K., Smith, N.C., Matthews, J.M.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP220101489
Australian Research Council (ARC)	Australia	DP190102543

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release