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- PDB-8ao0: Solution structure of nanoFAST/HBR-DOM2 complex -

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Basic information

Entry
Database: PDB / ID: 8ao0
TitleSolution structure of nanoFAST/HBR-DOM2 complex
ComponentsPhotoactive yellow protein
KeywordsFLUORESCENT PROTEIN / fluorogen-activating protein / FAST / nanoFAST / spatial structure / dynamics / ligand sepcificity / fluorogen / binding constatnt
Function / homology
Function and homology information


photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
Photoactive yellow-protein / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
Chem-O1F / Photoactive yellow protein
Similarity search - Component
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLushpa, V.A. / Goncharuk, M.V. / Goncharuk, S.A. / Baleeva, N.S. / Baranov, M.S. / Mineev, K.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation18-73-10105 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2022
Title: Spatial Structure of NanoFAST in the Apo State and in Complex with its Fluorogen HBR-DOM2.
Authors: Lushpa, V.A. / Baleeva, N.S. / Goncharuk, S.A. / Goncharuk, M.V. / Arseniev, A.S. / Baranov, M.S. / Mineev, K.S.
History
DepositionAug 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7872
Polymers12,4891
Non-polymers2971
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Photoactive yellow protein / PYP


Mass: 12489.214 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: pyp / Production host: Escherichia coli (E. coli) / References: UniProt: P16113
#2: Chemical ChemComp-O1F / (5~{Z})-5-[(2,5-dimethoxy-4-oxidanyl-phenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one


Mass: 297.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11NO4S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HNCA
1181isotropic13D HN(CO)CA
1171isotropic13D HN(CA)CO
1161isotropic13D TOCSY
1151isotropic13D (H)CCH-COSY
1141isotropic13D (H)CCH-TOCSY
1131isotropic13D 1H-13C NOESY
1121isotropic13D 1H-15N NOESY
1111isotropic13D HN(CA)CB
1101isotropic1hbCBcarHar

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Sample preparation

DetailsType: solid
Contents: 20 mM NaPi, 20 mM sodium chloride, 0.001 % sodium azide, 90% H2O/10% D2O
Label: 15N, 13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMNaPinatural abundance1
20 mMsodium chloridenatural abundance1
0.001 %sodium azidenatural abundance1
Sample conditionsIonic strength: NULL mM / Label: conditions_1 / pH: 7 / Pressure: AMBIENT Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
TopSpin3Bruker Biospinprocessing
qMDD3.2Maxim Mayzev, Krzysztof Kazimierczuk, Vladislav Orekhovprocessing
CARA1.9.1.7Keller and Wuthrichpeak picking
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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