+Open data
-Basic information
Entry | Database: PDB / ID: 7xh9 | |||||||||||||||||||||||||||||||
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Title | Crystal structure of a dimeric interlocked parallel G-quadruplex | |||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-quadruplex / interlocked | Function / homology | : / STRONTIUM ION / DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | Authors | Ngo, K.H. / Liew, C.W. / Lattmann, S. / Winnerdy, F.R. / Phan, A.T. | Funding support | Singapore, 2items |
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 | Title: Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A.G.G.G.G pentad in an interlocked G-quadruplex. Authors: Ngo, K.H. / Liew, C.W. / Lattmann, S. / Winnerdy, F.R. / Phan, A.T. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xh9.cif.gz | 57 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xh9.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/7xh9 ftp://data.pdbj.org/pub/pdb/validation_reports/xh/7xh9 | HTTPS FTP |
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-Related structure data
Related structure data | 7x7gC 7xdhSC 7xhdC 7xieC 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
#1: DNA chain | Mass: 5107.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-SR / #4: Water | ChemComp-HOH / | 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: 2.06 Å3/Da / Density % sol: 40.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.08 M Strontium chloride hexahydrate, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 7.0, 20% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953659 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953659 Å / Relative weight: 1 |
Reflection | Resolution: 1.586→20.33 Å / Num. obs: 9790 / % possible obs: 94.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.5 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.91 |
Reflection shell | Resolution: 1.586→1.642 Å / Num. unique obs: 961 / CC1/2: 0.922 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7XDH Resolution: 1.63→20.33 Å / SU ML: 0.2144 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.4293 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→20.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 6.77914808831 Å / Origin y: 22.3619387789 Å / Origin z: 12.33412235 Å
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Refinement TLS group | Selection details: all |