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- PDB-6xyv: NMR solution structure of the Iron-Sulfur protein PioC from Rhodo... -

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Basic information

Entry
Database: PDB / ID: 6xyv
TitleNMR 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
AuthorsCantini, F. / Trindade, I.
Funding support Portugal, Italy, 2items
OrganizationGrant numberCountry
European Union (EU)Horizon2020: 810856-TIMB3 Twin to illuminate metal in biology and biocatalysis through biospectroscopy Portugal
Instruct-ERIC4509 Italy
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
DepositionJan 31, 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 area340 Å2
ΔGint-20 kcal/mol
Surface area3960 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000target function
RepresentativeModel #1target function

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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
Details: This is a 4Fe-4S binding protein. The iron-sulphur cluster is named SF4 in the PDB.
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
112isotropic22D 1H-15N HSQC
122isotropic23D HNCO
132isotropic23D HNCA
142isotropic23D CBCANH
152isotropic23D CBCA(CO)NH
162isotropic23D HN(CA)CO
172isotropic23D HBHA(CO)NH
182isotropic23D HNHA
1122isotropic22D 1H-13C HSQC
1113isotropic12D 1H-1H TOCSY
1103isotropic22D 1H-1H NOESY
192isotropic23D (H)CCH-TOCSY
1164isotropic23D 1H-15N NOESY
1152isotropic43D 1H-13C NOESY aliphatic
1144isotropic32D relaxation experiments
1132isotropic52D CON

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution2500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O15N13C_sample90% H2O/10% D2O
solution3500 uM PioC, 90% H2O/10% D2Ounlabeled90% H2O/10% D2O
solution4150 uM [U-99% 15N] PioC, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMPioC[U-13C; U-15N]2
500 uMPioCnatural abundance3
150 uMPioC[U-99% 15N]4
Sample conditionsDetails: buffer: 20mM potassium phosphate 300mM NaCl pH 5.6 / Ionic strength: 300 mM / Label: conditions_allsamples / 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 AVANCE IIIBrukerAVANCE III9002
Bruker AVANCEBrukerAVANCE5003Console NEO
Bruker AVANCEBrukerAVANCE9504Console NEO
Bruker AVANCEBrukerAVANCE7005Console NEO

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Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
TopSpin3.16Bruker Biospincollection
TopSpin3.16Bruker Biospinprocessing
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Refinement
MethodSoftware ordinal
torsion angle dynamics2
molecular dynamics5
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 2000 / Conformers submitted total number: 20

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