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- PDB-6dwz: Hermes transposase deletion dimer complex with (C/G) DNA -

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Basic information

Entry
Database: PDB / ID: 6dwz
TitleHermes transposase deletion dimer complex with (C/G) DNA
Components
  • DNA (26-MER)
  • DNA (5'-D(*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)-3')
  • DNA (5'-D(*GP*CP*GP*TP*GP*AP*C)-3')
  • Hermes transposase
Keywordsdna binding protein/dna / transposase / DNA BINDING PROTEIN / dna binding protein-dna complex
Function / homology
Function and homology information


protein dimerization activity / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Zinc finger, BED domain-containing / : / Hermes trasposase, DNA-binding domain / Hermes transposase DNA-binding domain / HAT, C-terminal dimerisation domain / hAT family C-terminal dimerisation region / Zinc finger, BED-type / Zinc finger BED-type profile. / BED zinc finger / Arc Repressor Mutant, subunit A ...Zinc finger, BED domain-containing / : / Hermes trasposase, DNA-binding domain / Hermes transposase DNA-binding domain / HAT, C-terminal dimerisation domain / hAT family C-terminal dimerisation region / Zinc finger, BED-type / Zinc finger BED-type profile. / BED zinc finger / Arc Repressor Mutant, subunit A / Ribonuclease H-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Hermes transposase
Similarity search - Component
Biological speciesMusca domestica (house fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDyda, F. / Hickman, A.B.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase.
Authors: Hickman, A.B. / Voth, A.R. / Ewis, H. / Li, X. / Craig, N.L. / Dyda, F.
History
DepositionJun 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hermes transposase
B: DNA (5'-D(*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)-3')
C: DNA (26-MER)
D: DNA (5'-D(*GP*CP*GP*TP*GP*AP*C)-3')
E: Hermes transposase
F: DNA (5'-D(*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)-3')
G: DNA (26-MER)
H: DNA (5'-D(*GP*CP*GP*TP*GP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)147,5688
Polymers147,5688
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20860 Å2
ΔGint-166 kcal/mol
Surface area53680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.380, 121.110, 132.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hermes transposase


Mass: 59033.633 Da / Num. of mol.: 2 / Mutation: C519S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Musca domestica (house fly) / Production host: Escherichia coli (E. coli) / References: UniProt: Q25438
#2: DNA chain DNA (5'-D(*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)-3')


Mass: 4629.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Musca domestica (house fly)
#3: DNA chain DNA (26-MER)


Mass: 7983.107 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Musca domestica (house fly)
#4: DNA chain DNA (5'-D(*GP*CP*GP*TP*GP*AP*C)-3')


Mass: 2138.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Musca domestica (house fly)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 50 mM MES, 50 mM sodium acetate, 15% PEG MME2000 / PH range: 5.8-6.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 34628 / % possible obs: 99 % / Redundancy: 19.27 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 18.63
Reflection shellResolution: 2.9→2.98 Å / Rmerge(I) obs: 1.862 / Num. unique obs: 2544

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D1Q

4d1q


Resolution: 3.2→29.513 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 36.39
RfactorNum. reflection% reflection
Rfree0.2982 699 2.7 %
Rwork0.2025 --
obs0.2051 25884 99.09 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7664 1914 0 0 9578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0179954
X-RAY DIFFRACTIONf_angle_d1.73513836
X-RAY DIFFRACTIONf_dihedral_angle_d23.475708
X-RAY DIFFRACTIONf_chiral_restr0.0871574
X-RAY DIFFRACTIONf_plane_restr0.011416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.44680.36831360.24454918X-RAY DIFFRACTION98
3.4468-3.79310.40171380.25464953X-RAY DIFFRACTION99
3.7931-4.34040.35871390.22095009X-RAY DIFFRACTION99
4.3404-5.46280.27241400.20375069X-RAY DIFFRACTION100
5.4628-29.51450.23151460.1655236X-RAY DIFFRACTION99

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