[English] 日本語
Yorodumi- PDB-1s6j: N-terminal Region of the Ca2+-saturated calcium regulatory domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s6j | ||||||
---|---|---|---|---|---|---|---|
Title | N-terminal Region of the Ca2+-saturated calcium regulatory domain (CLD) from Soybean Calcium-dependent Protein Kinase-alpha (CDPK) | ||||||
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 / calmodulin-dependent protein kinase activity / calmodulin binding / non-specific serine/threonine protein kinase / 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: 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. #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: 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. #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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1s6j.cif.gz | 384.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1s6j.ent.gz | 333.3 KB | Display | PDB format |
PDBx/mmJSON format | 1s6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/1s6j ftp://data.pdbj.org/pub/pdb/validation_reports/s6/1s6j | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 9642.602 Da / Num. of mol.: 1 / Fragment: N-terminal region of calmodulin-like domain (CLD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) Description: 13 residues from an N-terminal His-tag, and the N-terminal domain of the Ca2+-regulatory region Gene: CDPK SK5 / Plasmid: pET-19b / 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 |
---|---|
#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
---|---|
NMR experiment | Type: 3D 15N-separated NOESY |
NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy |
-Sample preparation
Details |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Sample conditions | Ionic strength: 200 mM NaCl, 10 mM CaCl2 / pH: 6.9 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing; molecular dynamics; matrix relaxation Software ordinal: 1 Details: Based on 765 unambiguous NOE-derived restraints, 118 ambiguous NOE-derived restraints, 130 dihedral angle restraints (CSI and TALOS derived) | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the ...Conformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 15 |