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- PDB-4hj5: 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: 4hj5 | ||||||
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Title | Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGTTTCGGT) | ||||||
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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 | ![]() | 50.7 KB | Display | ![]() |
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PDB format | ![]() | 34 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 ![]() 4hikSC ![]() 4himC ![]() 4hioC ![]() 4hj7C ![]() 4hj8C ![]() 4hj9C ![]() 4hjaC C: citing same article ( S: Starting model for refinement |
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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: 17182.414 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: 2777.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: variation of S. pombe telomeric sequence / Source: (synth.) ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.33 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 35% PEG 6000, 0.2M sodium 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: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 7, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.04→50 Å / Num. all: 10598 / Num. obs: 9855 / % possible obs: 93 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.077 / Χ2: 1.88 / Net I/σ(I): 10.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HIK Resolution: 2.04→29.951 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.31 / σ(F): 0 / Phase error: 25.83 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.944 Å2 / ksol: 0.316 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.55 Å2 / Biso mean: 38.5819 Å2 / Biso min: 18.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→29.951 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: 7
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