+Open data
-Basic information
Entry | Database: PDB / ID: 2kx6 | ||||||
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Title | Signaling state of Photoactive Yellow Protein | ||||||
Components | Photoactive yellow protein | ||||||
Keywords | SIGNALING PROTEIN / SAXS / DEER / PYP intermediate / Signaling State / pB | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | Halorhodospira halophila (bacteria) | ||||||
Method | SOLUTION NMR / SOLUTION SCATTERING / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Ramachandran, P.L. / Lovett, J.E. / Carl, P.J. / Cammarata, M. / Lee, J.H. / Yang, J.O. / Ihee, H. / Timmel, C.R. / van Thor, J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2011 Title: The short-lived signaling state of the photoactive yellow protein photoreceptor revealed by combined structural probes. Authors: Ramachandran, P.L. / Lovett, J.E. / Carl, P.J. / Cammarata, M. / Lee, J.H. / Jung, Y.O. / Ihee, H. / Timmel, C.R. / van Thor, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kx6.cif.gz | 604.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kx6.ent.gz | 517.3 KB | Display | PDB format |
PDBx/mmJSON format | 2kx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/2kx6 ftp://data.pdbj.org/pub/pdb/validation_reports/kx/2kx6 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14350.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halorhodospira halophila (bacteria) / Strain: BN9626 / Gene: pyp / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16113 |
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#2: Chemical | ChemComp-HC4 / |
-Experimental details
-Experiment
Experiment |
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NMR experiment | Type: 2D 1H-15N HSQC |
-Sample preparation
Details |
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Sample |
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Sample conditions |
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-Data collection
NMR spectrometer | Type: Bruker Avance II / Manufacturer: Bruker / Model: Avance II / Field strength: 500 MHz |
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Soln scatter | Type: x-ray / Buffer name: 20 MM NACL / Conc. range: 64 mg/ml / Detector specific: Mar133: MAR RESEARCH / Detector type: CCD / Mean guiner radius: 1.46 nm / Sample pH: 7 / Source beamline: ID09B / Source class: Y / Source type: ESRF / Temperature: 293 K |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 15 / Conformers submitted total number: 14 | ||||||||||||
Soln scatter model | Conformer selection criteria: STRUCTUREs WITH THE LEAST RESTRAINT VIOLATIONS Num. of conformers calculated: 15 / Num. of conformers submitted: 14 / Representative conformer: 1 Software author list: Grishaev, Wu, Trewhella, Bax, Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warren Software list: CNS (NIH SAXS version) |