1ZR2 | pdb_00001zr2

Structure of a Synaptic gamma-delta Resolvase Tetramer Covalently Linked to two Cleaved DNAs

• PDB DOI: https://doi.org/10.2210/pdb1ZR2/pdb
• NAKB: 1ZR2

• Classification: recombination/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-05-18 Released: 2005-08-30 
• Deposition Author(s): Li, W., Kamtekar, S., Xiong, Y., Sarkis, G.J., Grindley, N.D., Steitz, T.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free: 
  0.322 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.264 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.270 (Depositor) 

Literature

Structure of a synaptic gamma delta resolvase tetramer covalently linked to two cleaved DNAs.

Li, W., Kamtekar, S., Xiong, Y., Sarkis, G.J., Grindley, N.D., Steitz, T.A.

(2005) Science 309: 1210-1215

• PubMed: 15994378 
• DOI: https://doi.org/10.1126/science.1112064
• Primary Citation Related Structures: 
  1ZR2, 1ZR4


• PubMed Abstract: 
  

  The structure of a synaptic intermediate of the site-specific recombinase gammadelta resolvase covalently linked through Ser10 to two cleaved duplex DNAs has been determined at 3.4 angstrom resolution. This resolvase, activated for recombination by mutations, forms a tetramer whose structure is substantially changed from that of a presynaptic complex between dimeric resolvase and the cleavage site DNA. Because the two cleaved DNA duplexes that are to be recombined lie on opposite sides of the core tetramer, large movements of both protein and DNA are required to achieve strand exchange. The two dimers linked to the DNAs that are to be recombined are held together by a flat interface. This may allow a 180 degrees rotation of one dimer relative to the other in order to reposition the DNA duplexes for strand exchange.

---

Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.05 kDa 
• Atom Count: 4,260 
• Modeled Residue Count: 435 
• Deposited Residue Count: 436 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Transposon gamma-delta resolvase	G [auth A], H [auth B]	183	Escherichia coli	Mutation(s): 6  Gene Names: tnpR
UniProt
Find proteins for P03012 (Escherichia coli (strain K12)) Explore P03012  Go to UniProtKB:  P03012

Entity ID: 1
Molecule	Chains	Length	Organism	Image
TCAGTGTCCGATAATTTAT	A [auth X], D [auth J]	19	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
AAA	B [auth Z], E [auth I]	3	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
TTATCGGACACTG	C [auth Y], F [auth K]	13	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free:  0.322 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.264 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.270 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.05	α = 90
b = 125.05	β = 90
c = 127.39	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-30 
Deposition Author(s): Li, W., Kamtekar, S., Xiong, Y., Sarkis, G.J., Grindley, N.D., Steitz, T.A.

Revision History  

• Version 1.0: 2005-08-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Data collection, Refinement description, Structure summary