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Open data
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Basic information
Entry | Database: PDB / ID: 5i2x | ||||||
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Title | Crystal Structure of TPP1 K170del | ||||||
![]() | Adrenocortical dysplasia protein homolog | ||||||
![]() | PROTEIN BINDING / OB fold | ||||||
Function / homology | ![]() positive regulation of single-stranded telomeric DNA binding / telomere assembly / segmentation / urogenital system development / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / shelterin complex / Telomere C-strand synthesis initiation / Telomere C-strand (Lagging Strand) Synthesis / positive regulation of telomere maintenance ...positive regulation of single-stranded telomeric DNA binding / telomere assembly / segmentation / urogenital system development / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / shelterin complex / Telomere C-strand synthesis initiation / Telomere C-strand (Lagging Strand) Synthesis / positive regulation of telomere maintenance / nuclear telomere cap complex / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / telomere capping / telomerase holoenzyme complex / embryonic limb morphogenesis / protein localization to chromosome, telomeric region / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / telomere maintenance via telomerase / DNA polymerase binding / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / : / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / positive regulation of telomere maintenance via telomerase / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / skeletal system development / intracellular protein transport / DNA Damage/Telomere Stress Induced Senescence / chromosome, telomeric region / nuclear body / protein-containing complex binding / nucleoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nandakumar, J. / Smith, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional consequences of a disease mutation in the telomere protein TPP1. Authors: Bisht, K. / Smith, E.M. / Tesmer, V.M. / Nandakumar, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.7 KB | Display | ![]() |
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PDB format | ![]() | 50.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.8 KB | Display | ![]() |
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Full document | ![]() | 433.6 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i2yC ![]() 2i46S S: Starting model for refinement 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 17429.354 Da / Num. of mol.: 2 / Fragment: OB domain / Mutation: deletion of amino acid K170 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.34 Å3/Da / Density % sol: 71.65 % / Mosaicity: 0.276 ° |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 3.6 M sodium formate, 100 mM Tris-Cl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 16, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03829 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 12617 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.059 / Rrim(I) all: 0.16 / Χ2: 1.496 / Net I/av σ(I): 14.929 / Net I/σ(I): 7.1 / Num. measured all: 86466 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2I46 Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.897 / SU B: 12.346 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.578 / ESU R Free: 0.312 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.16 Å2 / Biso mean: 37.111 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 3→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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