+Open data
-Basic information
Entry | Database: PDB / ID: 5lph | ||||||
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Title | Structure of the TOG domain of human Cep104 | ||||||
Components | Centrosomal protein of 104 kDaCentrosome | ||||||
Keywords | CELL CYCLE / TOG domain / HEAT repeat / Tubulin binding / Cep104 / Basal body / Centriole / Cilia | ||||||
Function / homology | Function and homology information thienylcyclohexylpiperidine binding / glutamate binding / glycine binding / centriole / cilium / spindle pole / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å | ||||||
Authors | van Breugel, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Structure / Year: 2017 Title: The Ciliopathy-Associated Cep104 Protein Interacts with Tubulin and Nek1 Kinase. Authors: Al-Jassar, C. / Andreeva, A. / Barnabas, D.D. / McLaughlin, S.H. / Johnson, C.M. / Yu, M. / van Breugel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lph.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lph.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/5lph ftp://data.pdbj.org/pub/pdb/validation_reports/lp/5lph | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 32590.248 Da / Num. of mol.: 2 / Fragment: TOG domain, UNP residues 392-676 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CEP104, KIAA0562 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O60308 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.58 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0 11 % PEG 20K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.94 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2014 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→49.5 Å / Num. obs: 40229 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.667 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.25→49.5 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.473 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.194 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.39 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→49.5 Å
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Refine LS restraints |
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