+Open data
-Basic information
Entry | Database: PDB / ID: 4kqb | |||||||||
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Title | crystal structure of the Golgi casein kinase with Mn/ADP bound | |||||||||
Components | Protein H03A11.1 | |||||||||
Keywords | TRANSFERASE / secreted kinase | |||||||||
Function / homology | Function and homology information Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / manganese ion binding / non-specific serine/threonine protein kinase / protein phosphorylation / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / extracellular region / ATP binding Similarity search - Function | |||||||||
Biological species | Caenorhabditis elegans (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.045 Å | |||||||||
Authors | Xiao, J. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Crystal structure of the Golgi casein kinase. Authors: Xiao, J. / Tagliabracci, V.S. / Wen, J. / Kim, S.A. / Dixon, J.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kqb.cif.gz | 358.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kqb.ent.gz | 297.5 KB | Display | PDB format |
PDBx/mmJSON format | 4kqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kqb_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4kqb_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4kqb_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 4kqb_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/4kqb ftp://data.pdbj.org/pub/pdb/validation_reports/kq/4kqb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 53065.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_H03A11.1, H03A11.1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9XTW2 |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 7 molecules
#4: Chemical | ChemComp-MN / #5: Chemical | #6: Chemical | ChemComp-NI / | |
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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: 2.22 Å3/Da / Density % sol: 44.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 12% PEG4000, 200 mM imidazole-malate (4:1), 3 mM NiCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.045→48.428 Å / Num. obs: 18134 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.045→48.428 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 26.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.045→48.428 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: 58.7313 Å / Origin y: 20.9562 Å / Origin z: 199.9055 Å
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Refinement TLS group | Selection details: all |