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Yorodumi- PDB-8g2n: Crystal structure of Tetrahymena thermophila G-rich DNA with nove... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g2n | ||||||
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Title | Crystal structure of Tetrahymena thermophila G-rich DNA with novel ligand PyDH2 | ||||||
Components | G-rich DNA | ||||||
Keywords | DNA / G-quadruplex DNA / ligand intercalation / four tetrads | ||||||
Function / homology | : / SPERMINE / : / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Martin, K.N. / Yatsunyk, L.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal structure of Tetrahymena thermophila G-rich DNA with novel ligand PyDH2 Authors: Martin, K.N. / Yatsunyk, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g2n.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g2n.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 8g2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/8g2n ftp://data.pdbj.org/pub/pdb/validation_reports/g2/8g2n | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-DNA chain , 1 types, 1 molecules A
#1: DNA chain | Mass: 7985.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote) |
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-Non-polymers , 5 types, 69 molecules
#2: Chemical | ChemComp-YSQ / Mass: 503.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H25N7O2 / Feature type: SUBJECT OF INVESTIGATION | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Chemical | ChemComp-SPM / | #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: 2.54 Å3/Da / Density % sol: 51.6 % / Description: Flat golden rhombus |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.02 M MgCl2, 0.165 M KCl, 0.04 M sodium cacodylate pH 6.5, 0.012 M spermine tetrahydrochloride, 39% (+/-)-2-Methyl-2,4-pentanediol (MPD) |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→29.78 Å / Num. obs: 18082 / % possible obs: 97.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 24.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.33→1.35 Å / Redundancy: 5.1 % / Num. unique obs: 818 / CC1/2: 0.758 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→29.78 Å / SU ML: 0.1461 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.1518 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: 31.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→29.78 Å
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Refine LS restraints |
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LS refinement shell |
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