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Yorodumi- PDB-8tc6: Sequence specific (AATT and TGTCA) orientation of netropsin and I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tc6 | ||||||||||||
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Title | Sequence specific (AATT and TGTCA) orientation of netropsin and ImPyPy molecules at two unique minor groove binding sites within a self-assembled 3D DNA lattice (4x5) | ||||||||||||
Components |
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Keywords | DNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold / Crystal Lattice / Minor Groove Binders / Netropsin / DAPI / Hoechst / ImPyPy / polyamide / host-guest | ||||||||||||
Function / homology | CACODYLATE ION / NETROPSIN / Chem-ZQQ / DNA / DNA (> 10) Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||||||||
Authors | Simmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Site-Specific Arrangement and Structure Determination of Minor Groove Binding Molecules in Self-Assembled Three-Dimensional DNA Crystals. Authors: Simmons, C.R. / Buchberger, A. / Henry, S.J.W. / Novacek, A. / Fahmi, N.E. / MacCulloch, T. / Stephanopoulos, N. / Yan, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tc6.cif.gz | 38.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tc6.ent.gz | 24.5 KB | Display | PDB format |
PDBx/mmJSON format | 8tc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tc6_validation.pdf.gz | 976.7 KB | Display | wwPDB validaton report |
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Full document | 8tc6_full_validation.pdf.gz | 983.8 KB | Display | |
Data in XML | 8tc6_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 8tc6_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/8tc6 ftp://data.pdbj.org/pub/pdb/validation_reports/tc/8tc6 | HTTPS FTP |
-Related structure data
Related structure data | 8t7bC 8t7xC 8t80C 8ta8C 8ta9C 8tajC 8tamC 8tapC 8taqC 8tb3C 8tb4C 8tb8C 8tbdC 8tboC 8tc2C 8tc4C 8tdtC 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
-DNA chain , 4 types, 4 molecules ABCD
#1: DNA chain | Mass: 6457.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 1480.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 2129.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 9 molecules
#5: Chemical | ChemComp-NT / | ||||
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#6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 3.41 Å3/Da / Density % sol: 63.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.5 mL of 0.05 M Na cacodylate pH 7.0 with 9 mM MgCl2, 2.25 mM spermine, 1.8 mM CoH18N6, 0.9 mM spermidine, and 5% PEG 400 was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock. Temp details: temperature gradient generated from 60 to 25 C at 0.3 degrees per hour |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→50 Å / Num. obs: 6739 / % possible obs: 100 % / Redundancy: 18.6 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.016 / Rrim(I) all: 0.066 / Χ2: 1.902 / Net I/σ(I): 7.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→43.76 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 47.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→43.76 Å
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Refine LS restraints |
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LS refinement shell |
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