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- PDB-2bzt: NMR structure of the bacterial protein YFHJ from E. coli -

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Basic information

Entry
Database: PDB / ID: 2bzt
TitleNMR structure of the bacterial protein YFHJ from E. coli
ComponentsPROTEIN ISCX
KeywordsIRON BINDING PROTEIN / IRON SULPHUR CLUSTERS / ISC OPERON / ISC PROTEINS
Function / homology
Function and homology information


enzyme inhibitor activity / iron-sulfur cluster assembly / ferrous iron binding / iron ion binding / cytosol
Similarity search - Function
IscX-like / ISC system FeS cluster assembly, IscX / IscX-like superfamily / Iron-sulphur cluster assembly / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / ARIA 1.2
AuthorsPastore, C. / Kelly, G. / Adinolfi, S. / Mc Cormick, J.E. / Pastore, A.
CitationJournal: Structure / Year: 2006
Title: YfhJ, a molecular adaptor in iron-sulfur cluster formation or a frataxin-like protein?
Authors: Pastore, C. / Adinolfi, S. / Huynen, M.A. / Rybin, V. / Martin, S. / Mayer, M. / Bukau, B. / Pastore, A.
History
DepositionAug 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary
Category: atom_site / citation ...atom_site / citation / pdbx_nmr_spectrometer / struct
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model / _struct.title
Revision 2.1Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN ISCX


Theoretical massNumber of molelcules
Total (without water)7,7381
Polymers7,7381
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein PROTEIN ISCX / PROTEIN YFHJ / YFHJ


Mass: 7737.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0C0L9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-13C NOESY-HSQC
221(H)CCH-TOCSY
3311H-15N NOESY-HSQC
4411H-15N TOCSY- -HSQC
551HNCO
661HNHA
771CBCA(CO)NH
881CBCAN
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED YFHJ

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Sample preparation

DetailsContents: 90% WATER/10% D2O, PHOSPHATE BUFFER 10MM
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 6.5 1.0 atm303.0 K
250 6.5 1.0 atm303.0 K
350 6.5 1.0 atm303.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2LINGE,HABECK,REIPING,NILGESrefinement
XEASYstructure solution
NMRDrawstructure solution
NMRPipestructure solution
RefinementMethod: ARIA 1.2 / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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