6TUU | pdb_00006tuu

Leishmania infantum Rad51 surrogate LiRadA10 in complex with 5,6,7,8-tetrahydro-2-naphthoic acid

• PDB DOI: https://doi.org/10.2210/pdb6TUU/pdb

• Classification: RECOMBINATION
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-01-08 Released: 2021-01-27 
• Deposition Author(s): Pantelejevs, T., Hyvonen, M.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.230 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Development of dedicated crystallographic systems for structure-guided drug discovery

Brear, P., Pantelejevs, T., Hyvonen, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 107.3 kDa 
• Atom Count: 7,514 
• Modeled Residue Count: 884 
• Deposited Residue Count: 972 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair and recombination protein RadA	A, B, C, D	243	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: radA, PF1926
UniProt
Find proteins for O74036 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore O74036  Go to UniProtKB:  O74036

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NY5 (Subject of Investigation/LOI)	F [auth A], H [auth B], I [auth C], K [auth D]	5,6,7,8-tetrahydronaphthalene-2-carboxylic acid C11 H12 O2 RSWXAGBBPCRION-UHFFFAOYSA-N
PO4	E [auth A], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.230 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.271	α = 90
b = 118.976	β = 91.42
c = 83.79	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
BUSTER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Pantelejevs, T., Hyvonen, M.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description