6PTL | pdb_00006ptl

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.271 (Depositor), 0.265 (DCC)
R-Value Work:
0.245 (Depositor), 0.249 (DCC)
R-Value Observed:
0.246 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6PTL

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P70662
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.271 (Depositor), 0.265 (DCC)
R-Value Work: 0.245 (Depositor), 0.249 (DCC)
R-Value Observed: 0.246 (Depositor)

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-22

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.