+Open data
-Basic information
Entry | Database: PDB / ID: 5xom | ||||||
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Title | Hydra Fam20 | ||||||
Components | Glycosaminoglycan xylosylkinase | ||||||
Keywords | TRANSFERASE / sugar protein kinase | ||||||
Function / homology | FAM20, C-terminal / FAM20 / Golgi casein kinase, C-terminal, Fam20 / phosphorylation / kinase activity / Golgi apparatus / membrane / Glycosaminoglycan xylosylkinase Function and homology information | ||||||
Biological species | Hydra vulgaris (swiftwater hydra) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Xiao, J. / Zhang, H. | ||||||
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 | 5xom.cif.gz | 305.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xom.ent.gz | 250.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/5xom ftp://data.pdbj.org/pub/pdb/validation_reports/xo/5xom | HTTPS FTP |
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-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: 45316.059 Da / Num. of mol.: 2 / Fragment: UNP residues 24-415 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hydra vulgaris (swiftwater hydra) / Gene: FAM20B / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: T2MHS6 #2: Sugar | ChemComp-NAG / #3: 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: 3.94 Å3/Da / Density % sol: 68.76 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.5 M (NH4)2SO4, 0.1 M BIS-TRIS propane, pH 7.0, and 3% dextran sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.997 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: CCD / Date: Oct 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 73294 / % possible obs: 99.7 % / Redundancy: 12.8 % / Net I/σ(I): 2.9 |
-Processing
Software |
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Refinement | Resolution: 2.2→30.806 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→30.806 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: -13.3735 Å / Origin y: -16.9242 Å / Origin z: 23.787 Å
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Refinement TLS group | Selection details: all |