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- PDB-3hos: Crystal structure of the mariner Mos1 paired end complex with Mg -

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Basic information

Entry
Database: PDB / ID: 3hos
TitleCrystal structure of the mariner Mos1 paired end complex with Mg
Components
  • Mos1 NTS inverted repeat DNA
  • Mos1 TS inverted repeat DNA
  • Transposable element mariner, complete cds
KeywordsTRANSFERASE / DNA BINDING PROTEIN/DNA / protein-DNA complex / synaptic complex / transposase / inverted repeat DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


DNA integration / endonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding / nucleus
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: 3.5 Å
AuthorsRichardson, J.M. / Walkinshaw, M.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Molecular architecture of the Mos1 paired-end complex: the structural basis of DNA transposition in a eukaryote
Authors: Richardson, J.M. / Colloms, S.D. / Finnegan, D.J. / Walkinshaw, M.D.
History
DepositionJun 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 16, 2013Group: Derived calculations
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
A: Transposable element mariner, complete cds
B: Transposable element mariner, complete cds
C: Mos1 NTS inverted repeat DNA
D: Mos1 TS inverted repeat DNA
E: Mos1 NTS inverted repeat DNA
F: Mos1 TS inverted repeat DNA
G: Mos1 NTS inverted repeat DNA
H: Mos1 TS inverted repeat DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,84911
Polymers130,6328
Non-polymers2163
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26220 Å2
ΔGint-168 kcal/mol
Surface area55610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.232, 85.033, 131.273
Angle α, β, γ (deg.)90.000, 98.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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: 4 / Auth seq-ID: 5 - 345 / Label seq-ID: 5 - 345

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transposable element mariner, complete cds / Mos1 transposase


Mass: 40865.316 Da / Num. of mol.: 2 / Mutation: T216A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila mauritiana (fry) / Gene: T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7JQ07, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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DNA chain , 2 types, 6 molecules CEGDFH

#2: DNA chain Mos1 NTS inverted repeat DNA


Mass: 7768.030 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Synthetic DNA
#3: DNA chain Mos1 TS inverted repeat DNA


Mass: 8532.542 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: SYnthetic DNA

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Non-polymers , 3 types, 5 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHESE RESIDUES WERE BASED ON THE NUCLEOTIDE SEQUENCE EMBL:X78906.

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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: 5.1168 Å3/Da / Density % sol: 75.9616 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9535 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. all: 33149 / Num. obs: 33149 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.5
Reflection shellResolution: 3.5→3.7 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.5 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
DMphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F7T

2f7t


Resolution: 3.5→29.87 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.887 / Occupancy max: 1 / Occupancy min: 1 / SU B: 61.746 / SU ML: 0.427 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.54 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1647 5.1 %RANDOM
Rwork0.219 ---
all0.222 32494 --
obs0.222 32494 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 254.39 Å2 / Biso mean: 70.567 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-4.04 Å2
2--3.54 Å20 Å2
3----5.43 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5614 3258 11 2 8885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0219421
X-RAY DIFFRACTIONr_bond_other_d0.0020.025556
X-RAY DIFFRACTIONr_angle_refined_deg1.9972.38413420
X-RAY DIFFRACTIONr_angle_other_deg0.943.00113581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1095669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20423.376311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.474151032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9831554
X-RAY DIFFRACTIONr_chiral_restr0.0910.21426
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021571
X-RAY DIFFRACTIONr_nbd_refined0.2940.33304
X-RAY DIFFRACTIONr_nbd_other0.3070.37181
X-RAY DIFFRACTIONr_nbtor_refined0.240.54247
X-RAY DIFFRACTIONr_nbtor_other0.1010.54104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.5491
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.130.524
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.324
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.55
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1960.51
X-RAY DIFFRACTIONr_mcbond_it28.78954261
X-RAY DIFFRACTIONr_mcbond_other8.48951338
X-RAY DIFFRACTIONr_mcangle_it33.6397.55432
X-RAY DIFFRACTIONr_scbond_it9.83528201
X-RAY DIFFRACTIONr_scangle_it13.8137988
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4860 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.640.5
MEDIUM THERMAL12.492
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 121 -
Rwork0.291 2271 -
all-2392 -
obs--98.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5680.190.2230.5886-0.13210.64420.16080.0452-0.0509-0.0182-0.0992-0.0014-0.0898-0.1329-0.0616-0.1090.086-0.0205-0.1231-0.0486-0.206629.9376-10.8092-2.1108
21.5609-1.17863.17841.8435-5.246915.32440.08450.3064-0.23370.0336-0.0326-0.0374-0.06041.1349-0.0519-0.02130.0201-0.08050.0032-0.0134-0.007643.6133-29.121664.4898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 345
2X-RAY DIFFRACTION1B5 - 345
3X-RAY DIFFRACTION1C4 - 28
4X-RAY DIFFRACTION1D29 - 56
5X-RAY DIFFRACTION1E4 - 28
6X-RAY DIFFRACTION1F29 - 56
7X-RAY DIFFRACTION2G4 - 28
8X-RAY DIFFRACTION2H29 - 56

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