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Yorodumi- PDB-1s6i: Ca2+-regulatory region (CLD) from soybean calcium-dependent prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s6i | ||||||
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Title | Ca2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence of Ca2+ and the junction domain (JD) | ||||||
Components | Calcium-dependent protein kinase SK5 | ||||||
Keywords | TRANSFERASE / PLANT PROTEIN / EF-hand / helix-loop-helix / calcium-binding / calmodulin superfamily | ||||||
Function / homology | Function and homology information calcium-dependent protein serine/threonine kinase activity / calcium/calmodulin-dependent protein kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / phosphorylation / protein serine kinase activity / calcium ion binding / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Glycine max (soybean) | ||||||
Method | SOLUTION NMR / simulated annealing; molecular dynamics; matrix relaxation | ||||||
Authors | Weljie, A.M. / Vogel, H.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Unexpected structure of the Ca2+-regulatory region from soybean calcium-dependent protein kinase-alpha Authors: Weljie, A.M. / Vogel, H.J. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Conformational changes in the Ca2+-regulatory region from soybean calcium-dependent protein kinase-alpha: fluorescence resonance energy transfer studies Authors: Weljie, A.M. / Robertson, K.M. / Vogel, H.J. #2: Journal: Biochemistry / Year: 2004 Title: Solution Structure and Backbone Dynamics of the N-Terminal Region of the Calcium Regulatory Domain from Soybean Calcium-Dependent Protein Kinase alpha Authors: Weljie, A.M. / Gagne, S.M. / Vogel, H.J. #3: Journal: Science / Year: 1991 Title: A calcium-dependent protein kinase with a regulatory domain similar to calmodulin Authors: Harper, J.F. / Sussman, M.R. / Schaller, G.E. / Putnam-Evans, C. / Charbonneau, H. / Harmon, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s6i.cif.gz | 828.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s6i.ent.gz | 690.9 KB | Display | PDB format |
PDBx/mmJSON format | 1s6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s6i_validation.pdf.gz | 346.3 KB | Display | wwPDB validaton report |
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Full document | 1s6i_full_validation.pdf.gz | 526 KB | Display | |
Data in XML | 1s6i_validation.xml.gz | 75.1 KB | Display | |
Data in CIF | 1s6i_validation.cif.gz | 100 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/1s6i ftp://data.pdbj.org/pub/pdb/validation_reports/s6/1s6i | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 21260.645 Da / Num. of mol.: 1 / Fragment: Calmodulin-like domain (CLD) and C-terminal tail Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) Description: Ca2+-binding region and C-terminal tail, along with His(6) at C-terminus Gene: CDPK SK5 / Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P28583, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy |
-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing; molecular dynamics; matrix relaxation Software ordinal: 1 Details: Based on 3051 unambiguous NOE-derived restraints, 1183 ambiguous NOE-derived restraints, 122 dihedral angle restraints (TALOS derived), 45 HN residual dipolar coupling restraints | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 15 |