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- PDB-4u7b: Crystal structure of a pre-cleavage Mos1 transpososome -

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Basic information

Entry
Database: PDB / ID: 4u7b
TitleCrystal structure of a pre-cleavage Mos1 transpososome
Components
  • DNA (25-MER)
  • DNA (31-MER)
  • Mariner Mos1 transposase
KeywordsHydrolase/DNA / transposase / transposon synaptic complex / helix-turn-helix / Rnase-H like fold / DNA transposition / hydrolase-dna complex
Function / homology
Function and homology information


mitotic DNA integrity checkpoint signaling / DNA topoisomerase binding / DNA double-strand break processing / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / replication fork processing / condensed chromosome / DNA integration / double-strand break repair via nonhomologous end joining ...mitotic DNA integrity checkpoint signaling / DNA topoisomerase binding / DNA double-strand break processing / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / replication fork processing / condensed chromosome / DNA integration / double-strand break repair via nonhomologous end joining / site of double-strand break / single-stranded DNA binding / double-stranded DNA binding / DNA recombination / Hydrolases; Acting on ester bonds / nucleus / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #1450 / Transposase, type 1 / Mos1 transposase, HTH domain / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Ribonuclease H-like superfamily/Ribonuclease H / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily ...Arc Repressor Mutant, subunit A - #1450 / Transposase, type 1 / Mos1 transposase, HTH domain / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Ribonuclease H-like superfamily/Ribonuclease H / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Mariner Mos1 transposase
Similarity search - Component
Biological speciesDrosophila mauritiana (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.09 Å
AuthorsRichardson, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust085176/Z/08/Z United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural role of the flanking DNA in mariner transposon excision.
Authors: Dornan, J. / Grey, H. / Richardson, J.M.
History
DepositionJul 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Dec 20, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (25-MER)
D: DNA (31-MER)
E: DNA (25-MER)
F: DNA (31-MER)
H: DNA (25-MER)
I: DNA (31-MER)
A: Mariner Mos1 transposase
B: Mariner Mos1 transposase
G: Mariner Mos1 transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,57812
Polymers173,2899
Non-polymers2883
Water362
1
C: DNA (25-MER)
D: DNA (31-MER)
E: DNA (25-MER)
F: DNA (31-MER)
A: Mariner Mos1 transposase
B: Mariner Mos1 transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,8149
Polymers115,5266
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23770 Å2
ΔGint-176 kcal/mol
Surface area48270 Å2
MethodPISA
2
H: DNA (25-MER)
I: DNA (31-MER)
G: Mariner Mos1 transposase

H: DNA (25-MER)
I: DNA (31-MER)
G: Mariner Mos1 transposase


Theoretical massNumber of molelcules
Total (without water)115,5266
Polymers115,5266
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area22610 Å2
ΔGint-137 kcal/mol
Surface area48800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.471, 340.090, 160.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31G

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 5 / Auth seq-ID: 5 - 345 / Label seq-ID: 2 - 342

Dom-IDAuth asym-IDLabel asym-ID
1AG
2BH
3GI

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Components

#1: DNA chain DNA (25-MER)


Mass: 7768.030 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Drosophila mauritiana (fry)
#2: DNA chain DNA (31-MER)


Mass: 9479.146 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Drosophila mauritiana (fry)
#3: Protein Mariner Mos1 transposase / Transposable element Mos1 transposase / Mos transposase


Mass: 40515.961 Da / Num. of mol.: 3 / Fragment: UNP residues 4-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila mauritiana (fry) / Gene: marinerT / Production host: Escherichia coli (E. coli)
References: UniProt: Q7JQ07, Hydrolases; Acting on ester bonds
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Ammonium acetate, 20 mM MgCl2, 50 mM Hepes pH 7.0, 5 % (w/v) PEG 8,000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.09→92.5 Å / Num. obs: 69135 / % possible obs: 99.7 % / Redundancy: 8 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 8.9
Reflection shellResolution: 3.09→3.27 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.4 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HOS

3hos


Resolution: 3.09→29.75 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / SU B: 22.348 / SU ML: 0.382 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.424
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 2441 5.1 %RANDOM
Rwork0.2284 45725 --
obs0.2301 48166 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 243.47 Å2 / Biso mean: 107.443 Å2 / Biso min: 54.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---4.24 Å20 Å2
3---4.34 Å2
Refinement stepCycle: final / Resolution: 3.09→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8575 3447 15 2 12039
Biso mean--169.16 80.54 -
Num. residues----1194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01712682
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210215
X-RAY DIFFRACTIONr_angle_refined_deg0.9691.68417864
X-RAY DIFFRACTIONr_angle_other_deg0.9433.00123619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.21251023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61823.27477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.914151581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7451584
X-RAY DIFFRACTIONr_chiral_restr0.0590.21713
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023012
X-RAY DIFFRACTIONr_mcbond_it4.77910.7434101
X-RAY DIFFRACTIONr_mcbond_other4.77910.7434100
X-RAY DIFFRACTIONr_mcangle_it7.85116.1065121
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2017MEDIUM POSITIONAL0.420.5
2B2017MEDIUM POSITIONAL0.40.5
3G2017MEDIUM POSITIONAL0.240.5
1A3589LOOSE POSITIONAL0.695
2B3589LOOSE POSITIONAL0.685
3G3589LOOSE POSITIONAL0.595
1A2017MEDIUM THERMAL9.982
2B2017MEDIUM THERMAL10.622
3G2017MEDIUM THERMAL11.032
1A3589LOOSE THERMAL10.7510
2B3589LOOSE THERMAL11.7510
3G3589LOOSE THERMAL11.3610
LS refinement shellResolution: 3.09→3.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 148 -
Rwork0.336 3084 -
all-3232 -
obs--90.86 %

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