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- PDB-6yrr: Heimdallarchaeota profilin -

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Basic information

Entry
Database: PDB / ID: 6yrr
TitleHeimdallarchaeota profilin
ComponentsProfilin
KeywordsSTRUCTURAL PROTEIN / Eukaryogenesis / profilin / Heimdallarchaeota
Function / homologyProfilin superfamily / Uncharacterized protein
Function and homology information
Biological speciesCandidatus Heimdallarchaeota archaeon LC_3 (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsCelestine, C.
CitationJournal: To Be Published
Title: Heimdallarchaea encodes profilin with eukaryotic-like actin regulation and polyproline binding
Authors: Celestine, C.
History
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 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: Profilin


Theoretical massNumber of molelcules
Total (without water)16,4951
Polymers16,4951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9510 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Profilin


Mass: 16494.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Heimdallarchaeota archaeon LC_3 (archaea)
Gene: HeimC3_27980 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9NL85

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1TROSY
121isotropic2HN(CA)CB
131isotropic2HN(CO)CACB
141isotropic2HNCA
151isotropic13D NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-99% 13C; U-99% 15N] profilin, 90% H2O/10% D2O
Label: 15N/13C sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: profilin / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 150 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 bar / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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