+Open data
-Basic information
Entry | Database: PDB / ID: 7ptb | ||||||
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Title | Crystal structure of the SPD-2 domain of human CEP192 | ||||||
Components | Centrosomal protein of 192 kDa | ||||||
Keywords | CELL CYCLE / Centriole / Centrosome / Cell-cycle / Pericentriolar material | ||||||
Function / homology | Function and homology information centrosome-templated microtubule nucleation / procentriole / procentriole replication complex / protein localization to centrosome / pericentriolar material / centriole replication / mitotic spindle assembly / phosphatase binding / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome ...centrosome-templated microtubule nucleation / procentriole / procentriole replication complex / protein localization to centrosome / pericentriolar material / centriole replication / mitotic spindle assembly / phosphatase binding / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / response to bacterium / Regulation of PLK1 Activity at G2/M Transition / centrosome / protein kinase binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å | ||||||
Authors | Rosa e Silva, I. / van Breugel, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Commun Biol / Year: 2022 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ptb.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ptb.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ptb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ptb_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 7ptb_full_validation.pdf.gz | 440.9 KB | Display | |
Data in XML | 7ptb_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 7ptb_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/7ptb ftp://data.pdbj.org/pub/pdb/validation_reports/pt/7ptb | HTTPS FTP |
-Related structure data
Related structure data | 7pt5C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: CEP192, KIAA1569, PP8407 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEP8 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97835 Å |
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: 0.97835 Å / Relative weight: 1 |
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 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.08→90.58 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.086 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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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