Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.77 kDa 
• Atom Count: 3817 
• Modelled Residue Count: 469 
• Deposited Residue Count: 556 
• Unique protein chains: 1

2GM5

An activated, truncated gamma-delta resolvase tetramer

• PDB DOI: 10.2210/pdb2GM5/pdb

• Classification: RECOMBINATION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-04-05 Released: 2006-06-27 
• Deposition Author(s): Kamtekar, S., Ho, R.S., Li, W., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.255 
• R-Value Work: 0.215 
• R-Value Observed: 0.219 

Literature

Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination.

Kamtekar, S., Ho, R.S., Cocco, M.J., Li, W., Wenwieser, S.V., Boocock, M.R., Grindley, N.D., Steitz, T.A.

(2006) Proc Natl Acad Sci U S A 103: 10642-10647

• PubMed: 16807292 
• DOI: 10.1073/pnas.0604062103
• Primary Citation of Related Structures:  
  2GM4, 2GM5


• PubMed Abstract: 
  

The structures of two mutants of the site-specific recombinase, gammadelta resolvase, that form activated tetramers have been determined. One, at 3.5-A resolution, forms a synaptic intermediate of resolvase that is covalently linked to two cleaved DNAs, whereas the other is of an unliganded structure determined at 2.1-A resolution. Comparisons of the four known tetrameric resolvase structures show that the subunits interact through the formation of a common core of four helices. The N-terminal halves of these helices superimpose well on each other, whereas the orientations of their C termini are more variable. The catalytic domains of resolvase in the unliganded structure are arranged asymmetrically, demonstrating that their positions can move substantially while preserving the four-helix core that forms the tetramer. These results suggest that the precleavage synaptic tetramer of gammadelta resolvase, whose structure is not known, may be formed by a similar four-helix core, but differ in the relative orientations of its catalytic and DNA-binding domains.

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Organizational Affiliation: 

Departments of Molecular Biophysics, and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transposon gamma-delta resolvase	A, B, C, D	139	Escherichia coli	Mutation(s): 9  Gene Names: tnpR
UniProt
Find proteins for P03012 (Escherichia coli (strain K12)) Explore P03012  Go to UniProtKB:  P03012

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.255 
• R-Value Work: 0.215 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.331	α = 90
b = 98.476	β = 90
c = 100.408	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-04-05 
• Released Date: 2006-06-27 
Deposition Author(s): Kamtekar, S., Ho, R.S., Li, W., Steitz, T.A.

Revision History  

• Version 1.0: 2006-06-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations