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- PDB-6dx0: Hermes transposase deletion dimer complex with (A/T) DNA -

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Basic information

Entry
Database: PDB / ID: 6dx0
TitleHermes transposase deletion dimer complex with (A/T) DNA
Components
  • DNA (25-MER)
  • DNA (5'-D(*AP*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*A)-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: 2.9 Å
AuthorsDyda, F. / Voth, A.R. / 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 (25-MER)
D: DNA (5'-D(*GP*CP*GP*TP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7905
Polymers73,7674
Non-polymers231
Water00
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 (25-MER)
D: DNA (5'-D(*GP*CP*GP*TP*GP*AP*A)-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 (25-MER)
D: DNA (5'-D(*GP*CP*GP*TP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,58010
Polymers147,5348
Non-polymers462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area22820 Å2
ΔGint-168 kcal/mol
Surface area54040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.600, 135.500, 102.850
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 (25-MER)


Mass: 7628.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Musca domestica (house fly)
#4: DNA chain DNA (5'-D(*GP*CP*GP*TP*GP*AP*A)-3')


Mass: 2162.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Musca domestica (house fly)
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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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: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 50 mM MES, 50 mM sodium acetate, 15% PEG MME 2000 / PH range: 5.8-6.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 19, 2016
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: 17367 / % possible obs: 90.5 % / Redundancy: 7.19 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.16
Reflection shellResolution: 2.9→2.98 Å / Rmerge(I) obs: 1.016 / Num. unique obs: 1395

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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: 2.9→28.438 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.86
RfactorNum. reflection% reflection
Rfree0.3046 869 5 %
Rwork0.2253 --
obs0.2292 17367 90.59 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 2.9→28.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 978 1 0 4867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085061
X-RAY DIFFRACTIONf_angle_d1.0017030
X-RAY DIFFRACTIONf_dihedral_angle_d20.072898
X-RAY DIFFRACTIONf_chiral_restr0.051798
X-RAY DIFFRACTIONf_plane_restr0.007719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.08160.49231570.32972985X-RAY DIFFRACTION100
3.0816-3.31920.36381570.26822981X-RAY DIFFRACTION99
3.3192-3.65260.34571180.25882238X-RAY DIFFRACTION77
3.6526-4.17970.34321140.25632172X-RAY DIFFRACTION82
4.1797-5.26060.3051600.22063028X-RAY DIFFRACTION99
5.2606-28.43960.24821630.18993094X-RAY DIFFRACTION98

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