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- PDB-4hik: Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ss... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hik | ||||||
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Title | Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGTTACGGT) | ||||||
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![]() | DNA BINDING PROTEIN / specificity / plasticity / promiscuity / OB-fold / ssDNA binding / single-stranded telomeric DNA | ||||||
Function / homology | ![]() Removal of the Flap Intermediate from the C-strand / telomere cap complex / chromosome, telomeric repeat region / telomerase inhibitor activity / shelterin complex / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping ...Removal of the Flap Intermediate from the C-strand / telomere cap complex / chromosome, telomeric repeat region / telomerase inhibitor activity / shelterin complex / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / telomere maintenance / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dickey, T.H. / Wuttke, D.S. | ||||||
![]() | ![]() Title: Nonspecific Recognition Is Achieved in Pot1pC through the Use of Multiple Binding Modes. Authors: Dickey, T.H. / McKercher, M.A. / Wuttke, D.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.5 KB | Display | ![]() |
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PDB format | ![]() | 35.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4hidC ![]() 4himC ![]() 4hioC ![]() 4hj5C ![]() 4hj7C ![]() 4hj8C ![]() 4hj9C ![]() 4hjaC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17369.996 Da / Num. of mol.: 1 Fragment: Pot1pC, partial DNA binding domain, residues 198-339 Mutation: V199D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972h- / Gene: pot1, SPAC26H5.06 / Plasmid: pTXB1 / Production host: ![]() ![]() |
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#2: DNA chain | Mass: 2786.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: telomeric single-stranded DNA / Source: (synth.) ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.93 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% w/V PEG 4000, 0.2M ammonium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Redundancy: 4.5 % / Av σ(I) over netI: 50.2 / Number: 179702 / Rmerge(I) obs: 0.041 / Χ2: 2.05 / D res high: 1.64 Å / D res low: 50 Å / Num. obs: 40149 / % possible obs: 99.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.636→50 Å / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.041 / Χ2: 2.05 / Net I/σ(I): 26.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||||||||||||||
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Phasing MAD | D res high: 1.74 Å / D res low: 5.74 Å / FOM : 0.704 / Reflection: 17982 | |||||||||||||||||||||
Phasing MAD set | Highest resolution: 5.74 Å / Lowest resolution: 1.74 Å
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.904 Å2 / ksol: 0.358 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.03 Å2 / Biso mean: 18.4056 Å2 / Biso min: 4.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.636→35.348 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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