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Yorodumi- PDB-4mdb: Structure of Mos1 transposase catalytic domain and Raltegravir with Mg -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mdb | ||||||
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Title | Structure of Mos1 transposase catalytic domain and Raltegravir with Mg | ||||||
Components | Mariner Mos1 transposase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / RNase-H fold / DDD motif / recombinase / DNA transposition / DNA integration / transposon DNA / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Richardson, J.M. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2014 Title: Structural Basis of Mos1 Transposase Inhibition by the Anti-retroviral Drug Raltegravir. Authors: Wolkowicz, U.M. / Morris, E.R. / Robson, M. / Trubitsyna, M. / 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 | 4mdb.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mdb.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 4mdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mdb_validation.pdf.gz | 820.3 KB | Display | wwPDB validaton report |
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Full document | 4mdb_full_validation.pdf.gz | 823.2 KB | Display | |
Data in XML | 4mdb_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 4mdb_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/4mdb ftp://data.pdbj.org/pub/pdb/validation_reports/md/4mdb | HTTPS FTP |
-Related structure data
Related structure data | 4mdaC 2f7tS C: citing same article (ref.) 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
#1: Protein | Mass: 26891.555 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 121-345) / Mutation: T216A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila mauritiana (fry) / Gene: mariner\T / Production host: Escherichia coli (E. coli) References: UniProt: Q7JQ07, Hydrolases; Acting on ester bonds | ||
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#2: Chemical | ChemComp-RLT / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.46 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 22% w/v PEG4000, 100 mM Tris, pH 6.8, 5 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-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 / Detector: PIXEL / Date: Feb 12, 2011 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.2 Å / Num. all: 23610 / Num. obs: 23539 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 4.7 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2F7T Resolution: 1.7→43.29 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.483 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 25.688 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→43.29 Å
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