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Yorodumi- PDB-6au4: Crystal structure of the major quadruplex formed in the human c-M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6au4 | |||||||||||||||||||||||||||||||||||||
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Title | Crystal structure of the major quadruplex formed in the human c-MYC promoter | |||||||||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / oncogene / quadruplex / c-MYC / promoter | Function / homology | : / DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | Authors | Stump, S. / Mou, T.C. / Sprang, S.R. / Natale, N.R. / Beall, H.D. | Funding support | United States, 4items |
Citation | Journal: PLoS ONE / Year: 2018 | Title: Crystal structure of the major quadruplex formed in the promoter region of the human c-MYC oncogene. Authors: Stump, S. / Mou, T.C. / Sprang, S.R. / Natale, N.R. / Beall, H.D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6au4.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6au4.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 6au4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/6au4 ftp://data.pdbj.org/pub/pdb/validation_reports/au/6au4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 7008.510 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | |
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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: 2.76 Å3/Da / Density % sol: 55.5 % / Description: Rectangular rod |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% MPD 300mM KCl 50mM LiCl 50mM Sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→35.03 Å / Num. obs: 6774 / % possible obs: 99.4 % / Redundancy: 12.6 % / Biso Wilson estimate: 55.55 Å2 / CC1/2: 1 / Rpim(I) all: 0.013 / Net I/σ(I): 34 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 652 / CC1/2: 0.966 / Rpim(I) all: 0.167 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WO2, 1XAV Resolution: 2.35→34.906 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→34.906 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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