9GSQ

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

• PDB DOI: https://doi.org/10.2210/pdb9GSQ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Leishmania major
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.212 
• R-Value Work: 0.174 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.99 kDa 
• Atom Count: 3,367 
• Modelled Residue Count: 375 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA binding domain of J-DNA binding protein 3	A, B	201	Leishmania major	Mutation(s): 0  Gene Names: LMJF_36_0390
UniProt
Find proteins for Q4Q239 (Leishmania major) Explore Q4Q239  Go to UniProtKB:  Q4Q239

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.212 
• R-Value Work: 0.174 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.701	α = 90
b = 40.937	β = 123.816
c = 100.595	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): de Vries, I., Adamopoulos, A., Joosten, R.P., Perrakis, A.

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

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release