[English] 日本語
Yorodumi- PDB-2kli: Structural Basis for the Photoconversion of A Phytochrome to the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kli | ||||||
---|---|---|---|---|---|---|---|
Title | Structural Basis for the Photoconversion of A Phytochrome to the Activated FAR-RED LIGHT-ABSORBING Form | ||||||
Components | Sensor protein | ||||||
Keywords | TRANSFERASE / Phytochrome / Kinase / Phosphoprotein / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG | ||||||
Function / homology | Function and homology information histidine kinase / phosphorelay sensor kinase activity / rhythmic process Similarity search - Function | ||||||
Biological species | Synechococcus sp. JA-2-3B'a | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Cornilescu, C.C. / Cornilescu, G. / Ulijasz, A.T. / Zhang, J. / Rivera, M. / Vierstra, R.D. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | Journal: Nature / Year: 2010 Title: Structural basis for the photoconversion of a phytochrome to the activated Pfr form Authors: Ulijasz, A.T. / Cornilescu, G. / Cornilescu, C.C. / Zhang, J. / Rivera, M. / Markley, J.L. / Vierstra, R.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2kli.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2kli.ent.gz | 949.2 KB | Display | PDB format |
PDBx/mmJSON format | 2kli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/2kli ftp://data.pdbj.org/pub/pdb/validation_reports/kl/2kli | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 19071.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. JA-2-3B'a(2-13) (bacteria) Gene: CYB_2465 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2JIZ5, histidine kinase |
---|---|
#2: Chemical | ChemComp-CYC / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1-2 mM [U-13C; U-15N] protein, 93% H2O/7% D2O / Solvent system: 93% H2O/7% D2O |
---|---|
Sample | Units: mM / Component: protein_1-1 / Isotopic labeling: [U-13C; U-15N] / Conc. range: 1-2 |
Sample conditions | Ionic strength: 10 / pH: 8.5 / Pressure: ambient / Temperature: 25 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
---|
-Processing
NMR software |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |