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- PDB-1xfn: NMR structure of the ground state of the photoactive yellow prote... -

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Basic information

Entry
Database: PDB / ID: 1xfn
TitleNMR structure of the ground state of the photoactive yellow protein lacking the N-terminal part
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / PAS DOMAIN
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 / torsion angle dynamics, simulated annealing
AuthorsBernard, C. / Houben, K. / Derix, N.M. / Marks, D. / van der Horst, M.A. / Hellingwerf, K.J. / Boelens, R. / Kaptein, R. / van Nuland, N.A.
CitationJournal: STRUCTURE / Year: 2005
Title: The solution structure of a transient photoreceptor intermediate: delta25 photoactive yellow protein
Authors: Bernard, C. / Houben, K. / Derix, N.M. / Marks, D. / van der Horst, M.A. / Hellingwerf, K.J. / Boelens, R. / Kaptein, R. / van Nuland, N.A.
History
DepositionSep 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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_software.name / _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)12,9802
Polymers12,8161
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)20 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Photoactive yellow protein / PYP


Mass: 12816.266 Da / Num. of mol.: 1 / Fragment: residues 26-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Production host: Escherichia coli (E. coli) / 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121CBCA(CO)NH
1323D 15N TOCSY-HSQC
1423D 15N-separated NOESY
1522D NOESY
1622D TOCSY
171HNCO
181HNACB
19113C filtered 2D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Delta25-PYP, 15N-13C, 50mM phosphate buffer90% H2O/10% D2O
21mM Delta25-PYP 15N, 50mM phosphate buffer90% H2O/10% D2O
Sample conditionsIonic strength: 50mM phosphate buffer / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE5002
Bruker AVANCEBrukerAVANCE7503

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1brukercollection
NMRPipejohnsinprocessing
CNS1.2Brungerstructure solution
CNS1.2Brungerrefinement
NMRView5.0.4Delagliodata analysis
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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