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Yorodumi- PDB-8edp: Crystal structure of a three-tetrad, parallel, and K+ stabilized ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8edp | ||||||||||||||||||||||||||||
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Title | Crystal structure of a three-tetrad, parallel, and K+ stabilized homopurine G-quadruplex from human chromosome 7 | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-quadruplex / parallel / propeller loops / three-tetrad | Function / homology | : / N-METHYLMESOPORPHYRIN / COBALT HEXAMMINE(III) / DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | Authors | Ye, M. / Yatsunyk, L.A. | Funding support | United States, 1items |
Citation | Journal: Bioorg.Med.Chem. / Year: 2022 | Title: Homopurine guanine-rich sequences in complex with N-methyl mesoporphyrin IX form parallel G-quadruplex dimers and display a unique symmetry tetrad. Authors: Ye, M. / Chen, E.V. / Pfeil, S.H. / Martin, K.N. / Atrafi, T. / Yun, S. / Martinez, Z. / 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 | 8edp.cif.gz | 45.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8edp.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 8edp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/8edp ftp://data.pdbj.org/pub/pdb/validation_reports/ed/8edp | HTTPS FTP |
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-Related structure data
Related structure data | 8eboC 4g0fS 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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 8009.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||||
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#2: Chemical | ChemComp-NCO / | ||||||
#3: Chemical | ChemComp-K / #4: Chemical | ChemComp-MMP / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.5 % Description: Red crystals in cubic, rhombus, or square prism shapes |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: 0.05M MES 6.5, 0.3M potassium chloride, 40% MPD, 0.005M Hexaammine cobalt chloride |
-Data collection
Diffraction | Mean temperature: 196 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→56.02 Å / Num. obs: 5027 / % possible obs: 98.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 62.16 Å2 / CC1/2: 0.986 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.01→2.06 Å / Num. unique obs: 374 / CC1/2: 0.447 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G0F Resolution: 2.01→28.01 Å / SU ML: 0.3468 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.99 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: 86.87 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→28.01 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: 2.76191104192 Å / Origin y: 15.4476523302 Å / Origin z: 4.58538821286 Å
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Refinement TLS group | Selection details: all |