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- PDB-7ava: Solution structure of the fluorogen-activating protein FAST in co... -

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Basic information

Entry
Database: PDB / ID: 7ava
TitleSolution structure of the fluorogen-activating protein FAST in complex with the ligand N871b
ComponentsFAST
KeywordsFLUORESCENT PROTEIN / Fluorogen-activating protein PAS domain
Function / homologyChem-S1Q
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsMineev, K.S. / Goncharuk, S.A. / Baranov, M.S.
CitationJournal: Chem Sci / Year: 2021
Title: NanoFAST: structure-based design of a small fluorogen-activating protein with only 98 amino acids.
Authors: Mineev, K.S. / Goncharuk, S.A. / Goncharuk, M.V. / Povarova, N.V. / Sokolov, A.I. / Baleeva, N.S. / Smirnov, A.Y. / Myasnyanko, I.N. / Ruchkin, D.A. / Bukhdruker, S. / Remeeva, A. / Mishin, ...Authors: Mineev, K.S. / Goncharuk, S.A. / Goncharuk, M.V. / Povarova, N.V. / Sokolov, A.I. / Baleeva, N.S. / Smirnov, A.Y. / Myasnyanko, I.N. / Ruchkin, D.A. / Bukhdruker, S. / Remeeva, A. / Mishin, A. / Borshchevskiy, V. / Gordeliy, V. / Arseniev, A.S. / Gorbachev, D.A. / Gavrikov, A.S. / Mishin, A.S. / Baranov, M.S.
History
DepositionNov 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5852
Polymers15,2491
Non-polymers3351
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8960 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein FAST


Mass: 15249.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-S1Q / (5~{Z})-5-[(2-methoxy-4-oxidanyl-phenyl)methylidene]-3-methyl-2-[(~{E})-2-pyridin-4-ylethenyl]imidazol-4-one


Mass: 335.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17N3O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY aromatic
121isotropic13D 1H-13C NOESY aromatic
131isotropic13D 1H-15N NOESY
141isotropic13D (H)CCH-TOCSY
151isotropic13D HNCO
161isotropic13D HN(CA)CB
171isotropic13D (H)CCH-TOCSY
181isotropic13D (H)CCH-COSY

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Sample preparation

DetailsType: solution
Contents: 0.85 mM [U-13C; U-15N] FAST, 0.90 mM N87, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 % sodium azide, 95% H2O/5% D2O
Label: H2O / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.85 mMFAST[U-13C; U-15N]1
0.90 mMN87natural abundance1
20 mMsodium phosphatenatural abundance1
20 mMsodium chloridenatural abundance1
0.01 %sodium azidenatural abundance1
Sample conditionsIonic strength: 40 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / 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
CARAKeller and Wuthrichchemical shift assignment
qMDDOrekhov, Mayzelprocessing
TALOS-NCornilescu, Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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