4DM0

TN5 transposase: 20MER OUTSIDE END 2 MN complex

• PDB DOI: https://doi.org/10.2210/pdb4DM0/pdb
• Entry: 4DM0 supersedes: 1MUR
• NAKB: 4DM0

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


• Deposited: 2012-02-06 Released: 2012-02-22 
• Deposition Author(s): Klenchin, V.A., Lovell, S., Goryshin, I.Y., Reznikoff, W.R., Rayment, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.203 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Two-metal active site binding of a TN5 transposase synaptic complex

Lovell, S., Goryshin, I.Y., Reznikoff, W.R., Rayment, I.

(2002) Nat Struct Biol 9: 278-281

• PubMed: 11896402 
• DOI: https://doi.org/10.1038/nsb778
• Primary Citation of Related Structures:  
  4DM0


• PubMed Abstract: 
  

  A synaptic complex of Tn5 transposase with an extended outside end DNA duplex was prepared and crystallized, and its crystal structure was determined in an effort to reveal the role of metal ions in catalysis. Two Mn2+ ions bound to the active site when a single nucleotide of donor DNA was added to the 3' end of the transferred strand. Marked conformational changes were observed in the DNA bases closest to the active site. The position of the metal ions and the conformational changes of the DNA provide insight into the mechanism of hairpin formation and cleavage, and is consistent with a two-metal model for catalysis.

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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 66.17 kDa 
• Atom Count: 4,785 
• Modelled Residue Count: 501 
• Deposited Residue Count: 518 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transposase for transposon Tn5	A	477	Escherichia coli	Mutation(s): 4  Gene Names: tnpA, tnp EC: 3.1
UniProt
Find proteins for Q46731 (Escherichia coli) Explore Q46731  Go to UniProtKB:  Q46731

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA TRANSFERRED STRAND	B	21	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA NON-TRANSFERRED STRAND	C	20	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	D [auth A], E [auth A], F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.203 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.378	α = 90
b = 112.378	β = 90
c = 232.783	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-22 
Deposition Author(s): Klenchin, V.A., Lovell, S., Goryshin, I.Y., Reznikoff, W.R., Rayment, I.
• This entry supersedes: 1MUR

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description