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)

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
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This is version 1.0 of the entry. See complete history.

Literature

Structure of the self-association domain of LDB2

Vu, T.H., Patel, K., Smith, N.C., Matthews, J.M.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O55203
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.