1MUH: CRYSTAL STRUCTURE OF TN5 TRANSPOSASE ...

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Data API 1MUH | pdb_00001muh

CRYSTAL STRUCTURE OF TN5 TRANSPOSASE COMPLEXED WITH TRANSPOSON END DNA

• PDB DOI: https://doi.org/10.2210/pdb1MUH/pdb
• Entry: 1MUH supersedes: 1F3I
• NAKB: 1MUH

• Classification: TRANSCRIPTION/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Deposited: 2002-09-23 Released: 2002-09-27 
• Deposition Author(s): Thoden, J.B., Holden, H.M., Davies, D.R., Goryshin, I.Y., Reznikoff, W.S., Rayment, I.

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.267 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history. LiteratureDownload Primary Citation 

•  Download Mendeley

Three-dimensional structure of the Tn5 synaptic complex transposition intermediate.

Davies, D.R., Goryshin, I.Y., Reznikoff, W.S., Rayment, I.

(2000) Science 289: 77-85

• PubMed: 10884228 Search on PubMed
• DOI: https://doi.org/10.1126/science.289.5476.77
• Primary Citation of Related Structures:  1MUH
• PubMed Abstract: 

  Genomic evolution has been profoundly influenced by DNA transposition, a process whereby defined DNA segments move freely about the genome. Transposition is mediated by transposases, and similar events are catalyzed by retroviral integrases such as human immunodeficiency virus-1 (HIV-1) integrase. Understanding how these proteins interact with DNA is central to understanding the molecular basis of transposition. We report the three-dimensional structure of prokaryotic Tn5 transposase complexed with Tn5 transposon end DNA determined to 2.3 angstrom resolution. The molecular assembly is dimeric, where each double-stranded DNA molecule is bound by both protein subunits, orienting the transposon ends into the active sites. This structure provides a molecular framework for understanding many aspects of transposition, including the binding of transposon end DNA by one subunit and cleavage by a second, cleavage of two strands of DNA by a single active site via a hairpin intermediate, and strand transfer into target DNA.

   View More
Organizational Affiliation: 
• Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.

Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (MN)

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (MN)

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

Biological assembly 1 assigned by authors.

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Macromolecule Content 

• Total Structure Weight: 66.19 kDa 
• Atom Count: 4,691 
• Modeled Residue Count: 495 
• Deposited Residue Count: 521 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

MacromoleculesProteins 1Nucleic Acids / Hybrid 2Find similar proteins by: Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tn5 transposase	C [auth A]	481	Escherichia coli	Mutation(s): 3 EC: 3.1
UniProt
Find proteins for Q46731 (Escherichia coli)Explore Q46731 Go to UniProtKB:  Q46731
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46731
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA TRANSFERRED STRAND	A [auth B]	20	N/A
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA NON-TRANSFERRED STRAND	B [auth C]	20	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MNQuery on MNDownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MANGANESE (II) IONMnWAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MGQuery on MGDownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM IONMgJLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.267 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 65 2 2Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.7	α = 90
b = 113.7	β = 90
c = 228.1	γ = 120

Software Package:

Software Name	Purpose
TNT	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental dataEntry History 

Deposition Data

• Released Date: 2002-09-27 
Deposition Author(s): Thoden, J.B., Holden, H.M., Davies, D.R., Goryshin, I.Y., Reznikoff, W.S., Rayment, I.
• This entry supersedes: 1F3I

Revision History (Full details and data files)

• Version 1.0: 2002-09-27Type: Initial release
• Version 1.1: 2008-04-28Changes: Version format compliance
• Version 1.2: 2011-07-13Changes: Version format compliance
• Version 1.3: 2019-07-24Changes: Data collection, Refinement description
• Version 1.4: 2021-10-27Changes: Database references, Derived calculations
• Version 1.5: 2024-02-14Changes: Data collection

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