+Open data
-Basic information
Entry | Database: PDB / ID: 5yh2 | ||||||
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Title | The structure of DrFam20C1 and hFam20A complex | ||||||
Components |
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Keywords | TRANSFERASE / complex / kinase | ||||||
Function / homology | Function and homology information tooth eruption / biomineral tissue development / phosphotransferase activity, alcohol group as acceptor / enamel mineralization / calcium ion homeostasis / protein serine/threonine kinase activator activity / response to bacterium / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of protein phosphorylation ...tooth eruption / biomineral tissue development / phosphotransferase activity, alcohol group as acceptor / enamel mineralization / calcium ion homeostasis / protein serine/threonine kinase activator activity / response to bacterium / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of protein phosphorylation / protein phosphorylation / protein serine/threonine kinase activity / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.55 Å | ||||||
Authors | Zhang, H. / Xiao, J. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structure and evolution of the Fam20 kinases Authors: Zhang, H. / Zhu, Q. / Cui, J. / Wang, Y. / Chen, M.J. / Guo, X. / Tagliabracci, V.S. / Dixon, J.E. / Xiao, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yh2.cif.gz | 345.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yh2.ent.gz | 280.9 KB | Display | PDB format |
PDBx/mmJSON format | 5yh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yh2_validation.pdf.gz | 927.8 KB | Display | wwPDB validaton report |
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Full document | 5yh2_full_validation.pdf.gz | 960.5 KB | Display | |
Data in XML | 5yh2_validation.xml.gz | 58.5 KB | Display | |
Data in CIF | 5yh2_validation.cif.gz | 78.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/5yh2 ftp://data.pdbj.org/pub/pdb/validation_reports/yh/5yh2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53464.199 Da / Num. of mol.: 2 / Fragment: UNP residues 63-529 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FAM20A, UNQ9388/PRO34279 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96MK3 #2: Protein | Mass: 64505.363 Da / Num. of mol.: 2 Mutation: T223A, K421M, A422D, L423M, H425I, Y426F, S427D, L428F, K429L, T430M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: fam20ca / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: E7FBB8 #3: Chemical | |
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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: 2.96 Å3/Da / Density % sol: 58.49 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 11% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 8% w/v Polyethylene glycol 10,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 3.55→50 Å / Num. obs: 35615 / % possible obs: 100 % / Redundancy: 11.4 % / Net I/σ(I): 11 |
-Processing
Software |
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Refinement | Resolution: 3.55→48.943 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.55→48.943 Å
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Refine LS restraints |
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LS refinement shell |
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