1FLO

FLP Recombinase-Holliday Junction Complex I

• PDB DOI: https://doi.org/10.2210/pdb1FLO/pdb
• NAKB: 1FLO

• Classification: ligase, lyase/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-08-14 Released: 2000-09-04 
• Deposition Author(s): Chen, Y., Narendra, U., Iype, L.E., Cox, M.M., Rice, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.297 
• R-Value Work: 0.249 
• R-Value Observed: 0.254 

Literature

Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping.

Chen, Y., Narendra, U., Iype, L.E., Cox, M.M., Rice, P.A.

(2000) Mol Cell 6: 885-897

• PubMed: 11090626 
• Primary Citation of Related Structures:  
  1FLO


• PubMed Abstract: 
  

  The crystal structure of a Flp recombinase tetramer bound to a Holliday junction intermediate has been determined at 2.65 A resolution. Only one of Flp's two domains, containing the active site, is structurally related to other lambda integrase family site-specific recombinases, such as Cre. The Flp active site differs, however, in that the helix containing the nucleophilic tyrosine is domain swapped, such that it cuts its DNA target in trans. The Flp tetramer displays pseudo four-fold symmetry matching that of the square planar Holliday junction substrate. This tetramer is stabilized by additional novel trans interactions among monomers. The structure illustrates how mechanistic unity is maintained on a chemical level while allowing for substantial variation on the structural level within a family of enzymes.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 235.1 kDa 
• Atom Count: 16,064 
• Modelled Residue Count: 1,752 
• Deposited Residue Count: 1,820 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FLP RECOMBINASE	I [auth A], J [auth B], K [auth C], L [auth D]	422	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: FLP1
UniProt
Find proteins for P03870 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P03870  Go to UniProtKB:  P03870

Entity ID: 1
Molecule	Chains	Length	Organism	Image
SYMMETRIZED FRT DNA SITES	A [auth E], C [auth G], E [auth I], G [auth K]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
SYMMETRIZED FRT DNA SITES	B [auth F], D [auth H], F [auth J], H [auth L]	20	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PHS	M [auth E], N [auth G], O [auth I], P [auth K]	PHOSPHONIC ACID H3 O3 P ABLZXFCXXLZCGV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.297 
• R-Value Work: 0.249 
• R-Value Observed: 0.254 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.48	α = 90
b = 180.18	β = 97.02
c = 98.6	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
MLPHARE	phasing
DM	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-09-04 
Deposition Author(s): Chen, Y., Narendra, U., Iype, L.E., Cox, M.M., Rice, P.A.

Revision History  

• Version 1.0: 2000-09-04
  Type: Initial release
  
• Version 1.1: 2007-10-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations