+Open data
-Basic information
Entry | Database: PDB / ID: 7xie | |||||||||||||||||||||||||||||||
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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 | : / DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 | 7xie.cif.gz | 34.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xie.ent.gz | 19.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/7xie ftp://data.pdbj.org/pub/pdb/validation_reports/xi/7xie | HTTPS FTP |
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-Related structure data
Related structure data | 7x7gC 7xdhSC 7xh9C 7xhdC 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: 5147.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | 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: 1.97 Å3/Da / Density % sol: 37.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.08 M Potassium chloride, 0.02 M Barium chloride dihydrate, 0.04 M Sodium cacodylate trihydrate pH 7.0, 40% 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: 1.97→26.33 Å / Num. obs: 5377 / % possible obs: 96.63 % / Redundancy: 3.5 % / Biso Wilson estimate: 32.29 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.63 |
Reflection shell | Resolution: 1.97→2.04 Å / Num. unique obs: 521 / CC1/2: 0.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7XDH Resolution: 1.97→26.33 Å / SU ML: 0.3026 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 33.0618 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: 34.55 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→26.33 Å
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Refine LS restraints |
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LS refinement shell |
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