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Yorodumi- PDB-8ipp: Crystal structure of the complex between an ankyrin and a paralle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ipp | |||||||||
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Title | Crystal structure of the complex between an ankyrin and a parallel G-quadruplex | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / G-quadruplex / DARPins / parallel / DNA BINDING PROTEIN-DNA COMPLEX | |||||||||
Function / homology | : / DNA / DNA (> 10) Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 Å | |||||||||
Authors | Ngo, K.H. / Liew, C.W. / Heddi, B. / Phan, A.T. | |||||||||
Funding support | Singapore, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2024 Title: Structural Basis for Parallel G-Quadruplex Recognition by an Ankyrin Protein. Authors: Ngo, K.H. / Liew, C.W. / Heddi, B. / 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 | 8ipp.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ipp.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ipp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/8ipp ftp://data.pdbj.org/pub/pdb/validation_reports/ip/8ipp | HTTPS FTP |
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-Related structure data
Related structure data | 8ipfC 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: 5131.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
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#2: Protein | Mass: 14864.692 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) | ||||||
#3: Chemical | #4: Chemical | #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: 2.71 Å3/Da / Density % sol: 54.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium chloride, 0.01 M magnesium chloride hexahydrate, 0.05 M MES monohydrate pH 5.6, 5% w/v polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953732 Å / Relative weight: 1 |
Reflection | Resolution: 2.007→38.41 Å / Num. obs: 14343 / % possible obs: 99.11 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 17.34 |
Reflection shell | Resolution: 2.01→2.082 Å / Num. unique obs: 1383 / CC1/2: 0.979 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.007→38.38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.96 / SU B: 10.58 / SU ML: 0.229 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.147 Details: Hydrogens have been used if present in the input file
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.066 Å2
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Refinement step | Cycle: LAST / Resolution: 2.007→38.38 Å
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Refine LS restraints |
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LS refinement shell |
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