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Yorodumi- PDB-2lb9: Refined solution structure of a cyanobacterial phytochrome gaf do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lb9 | ||||||
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Title | Refined solution structure of a cyanobacterial phytochrome gaf domain in the red light-absorbing ground state (corrected pyrrole ring planarity) | ||||||
Components | Sensor histidine kinase | ||||||
Keywords | TRANSFERASE / PCB / KINASE / GAF DOMAIN / PHOSPHOPROTEIN | ||||||
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 / molecular dynamics, torsion angle dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Cornilescu, C.C. / Cornilescu, G. / Ulijasz, A.T. / Vierstra, R.D. / Markley, J.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state. Authors: Cornilescu, G. / Ulijasz, A.T. / Cornilescu, C.C. / Markley, J.L. / Vierstra, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lb9.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2lb9.ent.gz | 919.9 KB | Display | PDB format |
PDBx/mmJSON format | 2lb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/2lb9 ftp://data.pdbj.org/pub/pdb/validation_reports/lb/2lb9 | HTTPS FTP |
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-Related 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: 23339.523 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) Strain: JA-2-3B'a(2-13) / Gene: CYB_2465 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2JIZ5 |
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#2: Chemical | ChemComp-CYC / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1-2 mM [U-13C; U-15N] protein, 93% H2O/7% D2O / Solvent system: 93% H2O/7% D2O |
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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: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics, 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 |