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Yorodumi- PDB-8ipf: Crystal structure of an ankyrin protein that can specifically rec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ipf | |||||||||
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Title | Crystal structure of an ankyrin protein that can specifically recognize a parallel G-quadruplex | |||||||||
Components | DARPin (2E4) | |||||||||
Keywords | DNA BINDING PROTEIN / G-quadruplex / parallel / DNA | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 | 8ipf.cif.gz | 200.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ipf.ent.gz | 160.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ipf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/8ipf ftp://data.pdbj.org/pub/pdb/validation_reports/ip/8ipf | 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: Protein | Mass: 14864.692 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: 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: 2.01 Å3/Da / Density % sol: 38.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 6% v/v ethylene glycol, 0.1 M citric acid pH 3.5, 10% w/v polyethylene glycol 6,000 |
-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: 0.95 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→49.25 Å / Num. obs: 62810 / % possible obs: 99.12 % / Redundancy: 2 % / Biso Wilson estimate: 28.98 Å2 / CC1/2: 1 / Net I/σ(I): 12.83 |
Reflection shell | Resolution: 2.01→2.082 Å / Num. unique obs: 6229 / CC1/2: 0.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→49.25 Å / SU ML: 0.1695 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.9907 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: 43.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→49.25 Å
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Refine LS restraints |
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LS refinement shell |
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