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- PDB-2kx6: Signaling state of Photoactive Yellow Protein -

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Basic information

Entry
Database: PDB / ID: 2kx6
TitleSignaling state of Photoactive Yellow Protein
ComponentsPhotoactive yellow protein
KeywordsSIGNALING 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
Photoactive yellow-protein / PAS domain / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-HYDROXYCINNAMIC ACID / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing
Model detailslowest energy, model 1
AuthorsRamachandran, P.L. / Lovett, J.E. / Carl, P.J. / Cammarata, M. / Lee, J.H. / Yang, J.O. / Ihee, H. / Timmel, C.R. / van Thor, J.
CitationJournal: 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
DepositionApr 27, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2012Group: Experimental preparation
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5142
Polymers14,3501
Non-polymers1641
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 15structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Photoactive yellow protein / PYP


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
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
Has protein modificationY

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
175 uM PYP, 50 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
275 uM PYP, 50 mM TRIS, 10 % glycerol, 50 mM Tris50 mM Tris
34.4 mM PYP, 50-200 mM Sodium phosphate, 20 mM sodium chloride, H2OH2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
75 uMPYP-11
50 mMpotassium phosphate-21
75 uMPYP-32
50 mMTRIS-42
10 %glycerol-52
4.4 mMPYP-63
mMSodium phosphate-750-2003
20 mMsodium chloride-83
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
105.75ambient 298 K
207.5ambient 50 K
3507ambient 298 K

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Data collection

NMR spectrometerType: Bruker Avance II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 500 MHz
Soln scatterType: 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
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
DEERANALYSIS2006Gunnar Jeschkedata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 15 / Conformers submitted total number: 14
Soln scatter modelConformer 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)

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