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Open data
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Basic information
Entry | Database: PDB / ID: 2kx6 | ||||||
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Title | Signaling state of Photoactive Yellow Protein | ||||||
![]() | Photoactive yellow protein | ||||||
![]() | SIGNALING PROTEIN / SAXS / DEER / PYP intermediate / Signaling State / pB | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / ![]() | ||||||
Model details | lowest energy, model 1 | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 604.4 KB | Display | ![]() |
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PDB format | ![]() | 517.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 373.7 KB | Display | ![]() |
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Full document | ![]() | 465.8 KB | Display | |
Data in XML | ![]() | 26.2 KB | Display | |
Data in CIF | ![]() | 46.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HC4 / |
-Experimental details
-Experiment
Experiment |
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NMR experiment | Type: 2D 1H-15N ![]() |
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Sample preparation
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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 |
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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) |