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- PDB-8ayg: Crystal structure of an intramolecular i-motif at the insulin-lin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ayg | ||||||
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Title | Crystal structure of an intramolecular i-motif at the insulin-linked polymorphic region (ILPR) | ||||||
![]() | Insulin-linked polymorphic region, ILPR DNA (31-MER) | ||||||
![]() | DNA / i-motif / promoter / insulin-linked polymorphic region | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Parkinson, G.N. / Alexandrou, E. / Waller, Z.A.E. / El-Omari, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of an intramolecular i-motif at the insulin-linked polymorphic region (ILPR) Authors: Parkinson, G.N. / Alexandrou, E. / Waller, Z.A.E. / El-Omari, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.1 KB | Display | ![]() |
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PDB format | ![]() | 28.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 388.2 KB | Display | ![]() |
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Full document | ![]() | 388.5 KB | Display | |
Data in XML | ![]() | 3.8 KB | Display | |
Data in CIF | ![]() | 4.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 9177.918 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.06 % / Description: pseudo-hexagonal |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2-Methyl-2,4-pentanediol (MPD), sodium chloride, sodium cacodylate, spermine (tetrachloride) PH range: 5.5 - 6.4 / Temp details: crystals can also be formed at 277.15K |
-Data collection
Diffraction | Mean temperature: 75 K / Ambient temp details: in vacuum (I23) / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 2, 2021 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 2.4797 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→47.42 Å / Num. obs: 8133 / % possible obs: 95.2 % / Redundancy: 44.5 % / Biso Wilson estimate: 76.91 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.024 / Rrim(I) all: 0.169 / Net I/σ(I): 30.4 / Num. measured all: 362297 / Scaling rejects: 17192 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.06 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→41.46 Å
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Refine LS restraints |
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LS refinement shell |
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