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- PDB-8c18: Solution structure of carotenoid-binding protein AstaPo1 in compl... -

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Basic information

Entry
Database: PDB / ID: 8c18
TitleSolution structure of carotenoid-binding protein AstaPo1 in complex with astaxanthin
ComponentsAstaxanthin binding fasciclin family protein
KeywordsTRANSPORT PROTEIN / PROTEIN / ASTAXANTHIN / CAROTENOID
Function / homologyFAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / ASTAXANTHIN / Astaxanthin binding fasciclin family protein
Function and homology information
Biological speciesCoelastrella astaxanthina (plant)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKornilov, F.D. / Savitskaya, A.G. / Slonimskiy, Y.B. / Goncharuk, S.A. / Sluchanko, N.N. / Mineev, K.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Federation President GrantMD-2834.2022.1.4 Russian Federation
CitationJournal: Commun Biol / Year: 2023
Title: Structural basis for the ligand promiscuity of the neofunctionalized, carotenoid-binding fasciclin domain protein AstaP.
Authors: Kornilov, F.D. / Slonimskiy, Y.B. / Lunegova, D.A. / Egorkin, N.A. / Savitskaya, A.G. / Kleymenov, S.Y. / Maksimov, E.G. / Goncharuk, S.A. / Mineev, K.S. / Sluchanko, N.N.
History
DepositionDec 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Astaxanthin binding fasciclin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2312
Polymers21,6341
Non-polymers5971
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, 3D 13C,15N-filtered,13C-edited-NOESY-HSQC
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1180 Å2
ΔGint-12 kcal/mol
Surface area14030 Å2
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 Astaxanthin binding fasciclin family protein


Mass: 21634.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coelastrella astaxanthina (plant) / Gene: astaP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S6BQ14
#2: Chemical ChemComp-AXT / ASTAXANTHIN / 3,3'-DIHYDROXY-BETA,BETA-CAROTENE-4,4'-DIONE / Astaxanthin


Mass: 596.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H52O4 / 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
111isotropic23D HNCA
1151isotropic22D 1H-13C HSQC aliphatic
1161isotropic22D 1H-15N HSQC
1171isotropic22D 1H-13C HSQC aromatic
121isotropic23D HN(CO)CA
131isotropic23D CBCA(CO)NH
241isotropic23D HNHB
2181isotropic22D 1H-13C HSQC aliphatic
2191isotropic22D 1H-15N HSQC
2201isotropic22D 1H-13C HSQC aromatic
2231isotropic12D 1H-13C HSQC aliphatic
2221isotropic12D 1H-15N HSQC
2211isotropic12D 1H-13C HSQC aromatic
151isotropic13D HNCO
161isotropic13D 1H-15N NOESY
171isotropic13D 1H-13C NOESY
181isotropic13D HN(CA)CO
191isotropic13D HN(CA)CB
1101isotropic13D (H)CCH-TOCSY
1271isotropic13D (H)CCH-COSY
2261isotropic12D 1H-13C HSQC aliphatic
2251isotropic12D 1H-15N HSQC
2241isotropic12D 1H-13C HSQC aromatic
2111isotropic13D 1H-13C NOESY
2121isotropic13D (H)CCH-TOCSY
2131isotropic13D 1H-15N NOESY
2141isotropic13D HNCO
2281isotropic13D (H)CCH-COSY

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Sample preparation

DetailsType: solution
Contents: 150 mM sodium chloride, 50 mM TRIS, 0.02 % w/v sodium azide, 250 uM [U-100% 13C; U-100% 15N] AstaPo1, 250 uM Astaxanthin, 95% H2O/5% D2O
Label: 13C15N_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 mMsodium chloridenatural abundance1
50 mMTRISnatural abundance1
0.02 % w/vsodium azidenatural abundance1
250 uMAstaPo1[U-100% 13C; U-100% 15N]1
250 uMAstaxanthinnatural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1200 mMcondition_2987.0 1 atm298 K
2200 mMcondition_3137.0 1 atm313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
qMDDMayzel, Kazimierczuk, Orekhovprocessing
TopSpinBruker Biospinprocessing
TALOS-NCornilescu, Baxdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
PyMOLSchrodinger, Inc.data analysis
RefinementMethod: torsion angle dynamics / 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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