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Yorodumi- PDB-2koi: Refined solution structure of a cyanobacterial phytochrome GAF do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2koi | ||||||
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Title | Refined solution structure of a cyanobacterial phytochrome GAF domain in the red light-absorbing ground state | ||||||
Components | Sensor protein | ||||||
Keywords | TRANSFERASE / PHYTOCHROME / GAF DOMAIN / PHYCOCYANOBILIN / PCB / BACTERIOPHYTOCHROME / CYANOBACTERIAL PHYTOCHROME / KINASE / PHOSPHOPROTEIN / PROTEIN STRUCTURE INITIATIVE / PSI-2 / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information histidine kinase / phosphorelay sensor kinase activity / rhythmic process Similarity search - Function | ||||||
Biological species | Synechococcus sp. (bacteria) | ||||||
Method | SOLUTION NMR / torsion angle molecular dynamics, internal variable dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Cornilescu, C.C. / Cornilescu, G. / Ulijasz, A.T. / 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. #1: 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 | 2koi.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2koi.ent.gz | 949.5 KB | Display | PDB format |
PDBx/mmJSON format | 2koi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/2koi ftp://data.pdbj.org/pub/pdb/validation_reports/ko/2koi | 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: 19071.775 Da / Num. of mol.: 1 / Fragment: GAF DOMAIN (UNP RESIDUES 31-200) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: JA-2-3B'a(2-13) / Gene: CYB_2465 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2JIZ5, histidine kinase |
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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 |
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Sample |
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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: torsion angle molecular dynamics, internal variable 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 |