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Yorodumi- PDB-8dwm: Host-guest complex of bleomycin A2 fully bound to CTTAGTTATAACTAAG -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dwm | ||||||
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Title | Host-guest complex of bleomycin A2 fully bound to CTTAGTTATAACTAAG | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / host-guest complex / Moloney murine leukemia virus reverse transcriptase / bleomycin A2 / DNA structure / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information host cell late endosome membrane / virion assembly / virion component / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination ...host cell late endosome membrane / virion assembly / virion component / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / structural constituent of virion / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Moloney murine leukemia virus synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.99 Å | ||||||
Authors | Georgiadis, M.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2023 Title: Two distinct rotations of bithiazole DNA intercalation revealed by direct comparison of crystal structures of Co(III)•bleomycin A 2 and B 2 bound to duplex 5'-TAGTT sites. Authors: Goodwin, K.D. / Lewis, M.A. / Long, E.C. / Georgiadis, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dwm.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dwm.ent.gz | 97.3 KB | Display | PDB format |
PDBx/mmJSON format | 8dwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/8dwm ftp://data.pdbj.org/pub/pdb/validation_reports/dw/8dwm | HTTPS FTP |
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-Related structure data
Related structure data | 8dw1C 8dw8C 1ztwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30023.531 Da / Num. of mol.: 1 / Fragment: N-terminal fragment (UNP residues 683-937) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moloney murine leukemia virus / Gene: gag-pro-pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UN00 |
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-DNA chain , 2 types, 2 molecules BG
#2: DNA chain | Mass: 2416.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 2434.643 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 5 molecules
#4: Chemical | ChemComp-3CO / |
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#5: Chemical | ChemComp-BLM / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.72 Å3/Da / Density % sol: 54.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Crystals of the host-guest complex were grown in 5 mM magnesium acetate, 0.05 M ADA pH 6.5, 9% PEG4000. To obtain complexes with BLM, crystals were soaked in well solutions containing 0.1 mM ...Details: Crystals of the host-guest complex were grown in 5 mM magnesium acetate, 0.05 M ADA pH 6.5, 9% PEG4000. To obtain complexes with BLM, crystals were soaked in well solutions containing 0.1 mM BLM followed by stabilization in 9% PEG4000, 5 mM magnesium acetate, 100 mM HEPES, pH 8.0, 20% ethylene glycol, 0.25 mM BLM until unit cell changes correlating with binding of BLM were detected. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.99→50 Å / Num. obs: 7774 / % possible obs: 94.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 50.97 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1.056 / Net I/σ(I): 12.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-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 1ZTW Resolution: 2.99→49.88 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 199.71 Å2 / Biso mean: 52.6544 Å2 / Biso min: 12.2 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.99→49.88 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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