+Open data
-Basic information
Entry | Database: PDB / ID: 7pt5 | ||||||
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Title | Crystal structure of the CH domain of human CEP44 | ||||||
Components | Centrosomal protein of 44 kDaCentrosome | ||||||
Keywords | CELL CYCLE / Centriole / Centrosome / Microtubule-associated protein | ||||||
Function / homology | Function and homology information centriole-centriole cohesion / centrosome cycle / centriole replication / centriole / spindle pole / midbody / microtubule binding / centrosome / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 | 7pt5.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pt5.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 7pt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/7pt5 ftp://data.pdbj.org/pub/pdb/validation_reports/pt/7pt5 | HTTPS FTP |
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-Related structure data
Related structure data | 7ptbC 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: 16753.955 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: amino acid residues GAMDP are residues of TEV protease cleavage Source: (gene. exp.) Homo sapiens (human) / Gene: CEP44, KIAA1712 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9C0F1 |
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#2: 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: 2.45 Å3/Da / Density % sol: 49.71 % |
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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 Hepes pH 7.3, 10% isopropanol, 10% PEG-4000. Crystals were mounted 0.1 M Hepes pH 7.5, 7.5% isopropanol, 30% PEG-400. |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97928 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97928 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→81.1 Å / Num. obs: 7159 / % possible obs: 100 % / Redundancy: 21.4 % / Biso Wilson estimate: 73.06 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.019 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 661 / Rpim(I) all: 0.506 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→33.62 Å / SU ML: 0.3315 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.7948 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 103.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→33.62 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 6.58776806038 Å / Origin y: 24.0539816559 Å / Origin z: 14.266926446 Å
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Refinement TLS group | Selection details: { A|* } |