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- PDB-2yon: Solution NMR structure of the C-terminal extension of two bacteri... -

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Basic information

Entry
Database: PDB / ID: 2yon
TitleSolution NMR structure of the C-terminal extension of two bacterial light, oxygen, voltage (LOV) photoreceptor proteins from Pseudomonas putida
ComponentsSENSORY BOX PROTEIN
KeywordsSIGNALING PROTEIN / VOLTAGE (LOV) DOMAIN
Function / homology
Function and homology information


PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
Biological speciesPSEUDOMONAS PUTIDA KT2440 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsRani, R. / Hartmann, R. / Lecher, J. / Krauss, U. / Jaeger, K. / Willbold, D.
CitationJournal: Biochemistry / Year: 2013
Title: Conservation of Dark Recovery Kinetic Parameters and Structural Features in the Pseudomonadaceae "Short" Light, Oxygen, Voltage (Lov) Protein Family: Implications for the Design of Lov-Based Optogenetic Tools.
Authors: Rani, R. / Jentzsch, K. / Lecher, J. / Hartmann, R. / Willbold, D. / Jaeger, K. / Krauss, U.
History
DepositionOct 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Atomic model / Other
Revision 1.3May 4, 2016Group: Atomic model / Derived calculations / Other
Revision 1.4Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr ..._pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SENSORY BOX PROTEIN


Theoretical massNumber of molelcules
Total (without water)3,4121
Polymers3,4121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 250LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide SENSORY BOX PROTEIN / ACESB2PEP


Mass: 3411.780 Da / Num. of mol.: 1 / Fragment: JALPHA HELIX, RESIDUES 123-151 / Source method: obtained synthetically / Details: N-TERMINAL ACETYLATION / Source: (synth.) PSEUDOMONAS PUTIDA KT2440 (bacteria) / References: UniProt: Q88JB0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED FROM PARTIAL MANUALLY ASSIGNED 1H-1H NOESY DATA OF SYNTHETIC PEPTIDE, ASSISTED BY AUTOMATED ASSIGNMENTS BY ARIA AND CALCULATED WITH CNS.

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Sample preparation

DetailsContents: 25% TRIFLUOROETHANOL/10% D2O/65% WATER
Sample conditionsIonic strength: 0.15 M / pH: 6.3 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
VnmrJ2.3Astructure solution
NMRPipe2012.114.11.33structure solution
ARIA2.3.1structure solution
CcpNmr Analysis2.2structure solution
CcpNmr Analysis2.1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 250 / Conformers submitted total number: 10

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