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- PDB-6dwy: Hermes transposase deletion dimer complex with (C/G) DNA and Ca2+ -

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Basic information

Entry
Database: PDB / ID: 6dwy
TitleHermes transposase deletion dimer complex with (C/G) DNA and Ca2+
Components
  • DNA (26-MER)
  • DNA (5'-D(*AP*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)-3')
  • DNA (5'-D(*C*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


nucleic acid metabolic process / protein dimerization activity / DNA binding / metal 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 / BED zinc finger / Zinc finger, BED-type / Zinc finger BED-type profile. / Arc Repressor Mutant, subunit A / Ribonuclease H-like superfamily ...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 / BED zinc finger / Zinc finger, BED-type / Zinc finger BED-type profile. / 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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(*AP*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)-3')
C: DNA (26-MER)
D: DNA (5'-D(*C*GP*CP*GP*TP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4275
Polymers74,3874
Non-polymers401
Water0
1
A: Hermes transposase
B: DNA (5'-D(*AP*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)-3')
C: DNA (26-MER)
D: DNA (5'-D(*C*GP*CP*GP*TP*GP*AP*C)-3')
hetero molecules

A: Hermes transposase
B: DNA (5'-D(*AP*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)-3')
C: DNA (26-MER)
D: DNA (5'-D(*C*GP*CP*GP*TP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,85310
Polymers148,7738
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area23490 Å2
ΔGint-168 kcal/mol
Surface area55190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.380, 135.350, 103.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hermes transposase


Mass: 59033.633 Da / Num. of mol.: 1 / 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(*AP*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)-3')


Mass: 4942.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Musca domestica (house fly)
#3: DNA chain DNA (26-MER)


Mass: 7983.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Musca domestica (house fly)
#4: DNA chain DNA (5'-D(*C*GP*CP*GP*TP*GP*AP*C)-3')


Mass: 2427.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Musca domestica (house fly)
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 50 mM MES pH 5.8-6.5, 50 mM sodium acetate, 15% PEG MME 2000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.5498 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 15708 / % possible obs: 99.5 % / Redundancy: 7.24 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 13.61
Reflection shellResolution: 3.1→3.18 Å / Rmerge(I) obs: 1.675 / Num. unique obs: 1152

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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→29.554 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 37.07
RfactorNum. reflection% reflection
Rfree0.2951 858 6 %
Rwork0.2591 --
obs0.2614 14296 99.65 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 978 1 0 4867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055058
X-RAY DIFFRACTIONf_angle_d0.7477030
X-RAY DIFFRACTIONf_dihedral_angle_d18.5812898
X-RAY DIFFRACTIONf_chiral_restr0.042798
X-RAY DIFFRACTIONf_plane_restr0.005719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.40030.36441390.32992179X-RAY DIFFRACTION99
3.4003-3.66240.34641410.32082216X-RAY DIFFRACTION100
3.6624-4.03020.37521420.30192214X-RAY DIFFRACTION100
4.0302-4.61140.33261420.28522234X-RAY DIFFRACTION99
4.6114-5.80270.32091440.26242252X-RAY DIFFRACTION100
5.8027-29.55550.2191500.20442343X-RAY DIFFRACTION100

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