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 ?
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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wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 697
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O55203
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 ?
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 ( ? )	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

View Full Validation Report

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

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.