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- PDB-7a58: NOE-only solution structure of the Iron-Sulfur protein PioC from ... -

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Basic information

Entry
Database: PDB / ID: 7a58
TitleNOE-only solution structure of the Iron-Sulfur protein PioC from Rhodopseudomonas palustris TIE-1
ComponentsPioC
KeywordsELECTRON TRANSPORT / iron-sulphur protein / paramagnetic protein / paramagnetic NMR / metallo proteins / solution structure by NMR
Function / homology
Function and homology information


aerobic electron transport chain / 4 iron, 4 sulfur cluster binding / electron transfer activity
Similarity search - Function
High potential iron-sulphur protein / High potential iron-sulphur protein superfamily / High potential iron-sulfur proteins family profile. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / PioC
Similarity search - Component
Biological speciesRhodopseudomonas palustris TIE-1 (phototrophic)
MethodSOLUTION NMR / torsion angle dynamics / molecular dynamics
AuthorsCantini, F. / Trindade, I.
Funding support Portugal, European Union, 2items
OrganizationGrant numberCountry
European Union (EU)Horizon2020: 810856-TIMB3 Twin to illuminate metal in biology and biocatalysis through biospectroscopy Portugal
European Commission810856European Union
CitationJournal: Febs J. / Year: 2021
Title: PRE-driven protein NMR structures: an alternative approach in highly paramagnetic systems.
Authors: Trindade, I.B. / Invernici, M. / Cantini, F. / Louro, R.O. / Piccioli, M.
History
DepositionAug 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PioC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2342
Polymers5,8831
Non-polymers3521
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, heteronuclear mobility data are also used to characterize protein aggregation statte
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area380 Å2
ΔGint-20 kcal/mol
Surface area4200 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000target function
RepresentativeModel #1closest to the average

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Components

#1: Protein PioC / Putative iron oxidase oxidoreductase protein


Mass: 5882.649 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris TIE-1 (phototrophic)
Gene: Rpal_0815 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1EBT4
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / 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
112isotropic42D 1H-15N HSQC
123isotropic63D HNCO
133isotropic63D HN(CA)CB
143isotropic33D 1H-15N NOESY
153isotropic63D HN(COCA)CB
173isotropic63D HN(CA)CO
163isotropic53D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1500 uM PioC, 90% H2O/10% D2Ounlabeled90% H2O/10% D2O
solution2500 uM [U-15N] PioC, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution3500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMPioCnatural abundance1
500 uMPioC[U-15N]2
500 uMPioC[U-13C; U-15N]3
Sample conditionsIonic strength: 300 mM / Label: ALL_SAMPLE / pH: 5.6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCEBrukerAVANCE4002
Bruker AVANCE IIIBrukerAVANCE III9005
Bruker AVANCEBrukerAVANCE5004
Bruker AVANCEBrukerAVANCE9503
Bruker AVANCEBrukerAVANCE7006

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Processing

NMR software
NameVersionDeveloperClassification
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
TopSpin3.6Bruker Biospinprocessing
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonrefinement
Refinement
MethodSoftware ordinal
torsion angle dynamics2
molecular dynamics1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 2000 / Conformers submitted total number: 20

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