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- PDB-7a4l: PRE-only solution structure of the Iron-Sulfur protein PioC from ... -

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Basic information

Entry
Database: PDB / ID: 7a4l
TitlePRE-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 / homologyHigh potential iron-sulphur protein / High potential iron-sulphur protein superfamily / High potential iron-sulfur proteins family profile. / aerobic electron transport chain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / electron transfer activity / IRON/SULFUR CLUSTER / PioC
Function and homology information
Biological speciesRhodopseudomonas palustris TIE-1 (phototrophic)
MethodSOLUTION NMR / torsion angle dynamics / molecular dynamics
AuthorsTrindade, I. / Invernici, M. / Cantini, F. / Louro, R. / Piccioli, M.
Funding support Portugal, 1items
OrganizationGrant numberCountry
European Union (EU)Horizon2020: 810856-TIMB3 Twin to illuminate metal in biology and biocatalysis through biospectroscopy Portugal
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 19, 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
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area330 Å2
ΔGint-20 kcal/mol
Surface area4090 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 / 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
115isotropic52D 1H-15N HSQC
124isotropic33D HNCO
174isotropic33D HN(CA)CO
134isotropic33D HN(CA)CB
164isotropic33D HN(COCA)CB
144isotropic23D 1H-15N NOESY
154isotropic43D 1H-13C NOESY
184isotropic32D CON
192isotropic22D NOESY
1102isotropic12D TOCSY
1115isotropic52D relaxation experiment
1124isotropic62D 15N-IR-HSQC AP
1134isotropic62D R2-weighted 15N-HSQC-AP

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution2500 uM PioC, 90% H2O/10% D2Ounlabeled90% H2O/10% D2O
solution5500 uM [U-15N] PioC, 90% H2O/10% D2O15_sample90% H2O/10% D2O
solution4500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMPioCnatural abundance2
500 uMPioC[U-15N]5
500 uMPioC[U-13C; U-15N]4
Sample conditionsDetails: These conditions are the same for all the NMR samples
Ionic strength: 300 mM / Label: ALL SAMPLES / pH: 5.6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCEBrukerAVANCE4006
Bruker AVANCE IIIBrukerAVANCE III9002
Bruker AVANCEBrukerAVANCE5005Console NEO
Bruker AVANCEBrukerAVANCE9504Console NEO
Bruker AVANCEBrukerAVANCE7003Console NEO

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Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
TopSpin3.6Bruker Biospinprocessing
Refinement
MethodSoftware ordinal
torsion angle dynamics2
molecular dynamics3
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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