+Open data
-Basic information
Entry | Database: PDB / ID: 5hoo | ||||||
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Title | Crystal structure of the Mos1 Strand Transfer Complex | ||||||
Components |
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Keywords | DNA / protein-DNA complex / DNA transposase / recombinase / integrase / helix-turn-helix / base flipping | ||||||
Function / homology | Function and homology information mitotic DNA integrity checkpoint signaling / DNA topoisomerase binding / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / DNA double-strand break processing / 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 / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / DNA double-strand break processing / histone H3K4 methyltransferase activity / replication fork processing / condensed chromosome / DNA integration / double-strand break repair via nonhomologous end joining / single-stranded DNA binding / site of double-strand break / double-stranded DNA binding / DNA recombination / Hydrolases; Acting on ester bonds / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Drosophila mauritiana (fry) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å | ||||||
Model details | represents the Mos1 transposition machinery after transposon integration into target DNA | ||||||
Authors | Richardson, J.M. / Morris, E.R. | ||||||
Citation | Journal: Elife / Year: 2016 Title: A bend, flip and trap mechanism for transposon integration. Authors: Morris, E.R. / Grey, H. / McKenzie, G. / Jones, A.C. / Richardson, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hoo.cif.gz | 435.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hoo.ent.gz | 354.5 KB | Display | PDB format |
PDBx/mmJSON format | 5hoo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hoo_validation.pdf.gz | 460.8 KB | Display | wwPDB validaton report |
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Full document | 5hoo_full_validation.pdf.gz | 466.6 KB | Display | |
Data in XML | 5hoo_validation.xml.gz | 27 KB | Display | |
Data in CIF | 5hoo_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/5hoo ftp://data.pdbj.org/pub/pdb/validation_reports/ho/5hoo | HTTPS FTP |
-Related structure data
Related structure data | 3hosS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40865.316 Da / Num. of mol.: 2 / Fragment: full-length Mos1 transposase / Mutation: T216A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila mauritiana (fry) / Gene: mariner / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7JQ07, Hydrolases; Acting on ester bonds |
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-DNA chain , 3 types, 6 molecules CEDFGH
#2: DNA chain | Mass: 7768.030 Da / Num. of mol.: 2 / Fragment: Mos1 IR DNA NTS / Source method: obtained synthetically / Details: synthetic DNA / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 11044.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA Source: (synth.) synthetic construct (others), (synth.) Drosophila mauritiana (fry) #4: DNA chain | Mass: 3005.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 2 types, 4 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.73 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% (v/v) MPD, 0.1 M sodium cacodylate pH 6.5,0.2 M magnesium acetate tetrahydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.29→86.99 Å / Num. obs: 25201 / % possible obs: 99.6 % / Redundancy: 3.1 % / Rsym value: 0.077 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 3.29→3.52 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.152 / % possible all: 99.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HOS Resolution: 3.3→60.01 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.943 / SU B: 90.635 / SU ML: 0.582 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.55 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145 Å2 / Biso mean: 73.034 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: final / Resolution: 3.3→60.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.385 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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