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- PDB-6dww: Hermes transposase deletion dimer complex with (A/T) DNA and Mn2+ -

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Basic information

Entry
Database: PDB / ID: 6dww
TitleHermes transposase deletion dimer complex with (A/T) DNA and Mn2+
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: 2.851 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)73,9327
Polymers73,7674
Non-polymers1653
Water1,33374
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)147,86414
Polymers147,5348
Non-polymers3306
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area23840 Å2
ΔGint-176 kcal/mol
Surface area54230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.480, 136.460, 104.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#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) / Strain (production host): RosettaBlue(DE3) / References: UniProt: Q25438

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DNA chain , 3 types, 3 molecules BCD

#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)

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Non-polymers , 2 types, 77 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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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: 58.44 %
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: 1.5498031 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498031 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 20430 / % possible obs: 99.7 % / Redundancy: 7.31 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.44
Reflection shellResolution: 2.85→2.92 Å / Rmerge(I) obs: 0.618 / Num. unique obs: 1476

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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: 2.851→29.803 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.79
RfactorNum. reflection% reflection
Rfree0.264 920 4.5 %
Rwork0.1992 --
obs0.202 20430 98.28 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 2.851→29.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 978 3 74 4943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045062
X-RAY DIFFRACTIONf_angle_d0.6447030
X-RAY DIFFRACTIONf_dihedral_angle_d18.5872898
X-RAY DIFFRACTIONf_chiral_restr0.039798
X-RAY DIFFRACTIONf_plane_restr0.004719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8507-3.00080.41991190.34672463X-RAY DIFFRACTION89
3.0008-3.18860.34451300.27412799X-RAY DIFFRACTION100
3.1886-3.43450.33931270.23822795X-RAY DIFFRACTION100
3.4345-3.77950.3171370.23122810X-RAY DIFFRACTION100
3.7795-4.3250.30071350.18992832X-RAY DIFFRACTION100
4.325-5.44360.23421330.16692852X-RAY DIFFRACTION100
5.4436-29.80430.17671390.16162959X-RAY DIFFRACTION100

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