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- PDB-1soy: Solution structure of the bacterial frataxin orthologue, CyaY -

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Basic information

Entry
Database: PDB / ID: 1soy
TitleSolution structure of the bacterial frataxin orthologue, CyaY
ComponentsCyaY protein
KeywordsUNKNOWN FUNCTION / Frataxin / Friedreich's ataxia iron binding
Function / homology
Function and homology information


iron-sulfur cluster assembly / ferric iron binding / ferrous iron binding / cytosol / cytoplasm
Similarity search - Function
: / Frataxin/CyaY / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily ...: / Frataxin/CyaY / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Iron-sulfur cluster assembly protein CyaY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsNair, M. / Adinolfi, S. / Pastore, C. / Kelly, G. / Temussi, P. / Pastore, A.
CitationJournal: Structure / Year: 2004
Title: Solution Structure of the Bacterial Frataxin Ortholog, CyaY; Mapping the Iron Binding Sites
Authors: Nair, M. / Adinolfi, S. / Pastore, C. / Kelly, G. / Temussi, P. / Pastore, A.
History
DepositionMar 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CyaY protein


Theoretical massNumber of molelcules
Total (without water)12,3701
Polymers12,3701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 250structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein CyaY protein


Mass: 12370.487 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CYAY, B3807 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27838

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
1213D 13C-separated NOESY
132HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM CyaY U-15N,13C, 50mM Phosphate buffer, 150mM KCl, 1mM DTT, 0.05%NaN390% H2O/10% D2O
20.5mM CyaY 15N, 50mM Phosphate buffer, 150mM KCl, 1mM DTT, 0.05%NaN390% H2O/10% D2O
Sample conditionsIonic strength: 150mM KCl / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Varian UNITYPLUSVarianUNITYPLUS6002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA8004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6Guntertstructure solution
X-PLOR2.8.1Brungerrefinement
NMRPipe3/2002Delaglioprocessing
XEASY1.2Bartelsdata analysis
Sparky3Goddard T.D.data analysis
MOLMOL2K.1Koradidata analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: Structures are based on a total of 902 NOE distance restraints, 138 dihedral angle restraints and 46 hydrogen bond restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 20

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