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Open data
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Basic information
Entry | Database: PDB / ID: 7ptb | ||||||
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Title | Crystal structure of the SPD-2 domain of human CEP192 | ||||||
![]() | Centrosomal protein of 192 kDa![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() centrosome-templated microtubule nucleation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rosa e Silva, I. / van Breugel, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural validation and assessment of AlphaFold2 predictions for centrosomal and centriolar proteins and their complexes. Authors: van Breugel, M. / Rosa E Silva, I. / Andreeva, A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.1 KB | Display | ![]() |
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PDB format | ![]() | 61.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7pt5C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 39340.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The GP residues on the N-terminus were left after PreScission protease cleavage. Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.19 % |
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Crystal grow![]() | Temperature: 292.15 K / Method: vapor diffusion Details: 100 nl protein solution and 100 nl of reservoir solution which was 0.1 M Na-Acetate pH 5.3, 3.9 M ammonium ni-trate. Crystals were mounted in 0.1 M Na-Acetate pH 4.6, 1 M ammonium nitrate, 30% glycerol. |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.08→90.6 Å / Num. obs: 33669 / % possible obs: 100 % / Redundancy: 18.6 % / Rpim(I) all: 0.024 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.08→2.14 Å / Redundancy: 2.5 % / Num. unique obs: 32002 / Rpim(I) all: 0.357 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.671 Å2
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Refinement step | Cycle: 1 / Resolution: 2.08→90.58 Å
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Refine LS restraints |
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