9GSO

DNA binding domain of J-DNA Binding Protein 3 (JBP3)

PDB DOI: https://doi.org/10.2210/pdb9GSO/pdb

Classification: TRANSCRIPTION
Organism(s): Leishmania tarentolae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-16 Released: 2024-09-25
Deposition Author(s): de Vries, I., Adamopoulos, A., Joosten, R.P., Perrakis, A.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.222
R-Value Work: 0.190

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Base-J binding proteins JBP1 and JBP3 have conserved structures of their J-DNA binding domain but drastically different affinities

de Vries, I., Adamopoulos, A., Kazokaite, J., Heidebrecht, T., Fish, A., Celie, P.N.H., Joosten, R.P., Perrakis, A.

To be published.

Macromolecule Content

Total Structure Weight: 20.68 kDa
Atom Count: 1,536
Modelled Residue Count: 167
Deposited Residue Count: 177
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA binding domain of J-DNA Binding Protein 3 (JBP3)	A	177	Leishmania tarentolae	Mutation(s): 0 Gene Names: LtaPh_3603800
UniProt
Find proteins for A0A640KTL4 (Leishmania tarentolae) Explore A0A640KTL4 Go to UniProtKB: A0A640KTL4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A640KTL4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.222
R-Value Work: 0.190
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.828	α = 90
b = 59.678	β = 90
c = 67.288	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing
PDB-REDO	refinement

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-25

Deposition Author(s):

Adamopoulos, A.

Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	714.014.002

Revision History (Full details and data files)

Version 1.0: 2024-09-25
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 R01GM133198.