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- PDB-1yka: Solution structure of Grx4, a monothiol glutaredoxin from E. coli. -

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Basic information

Entry
Database: PDB / ID: 1yka
TitleSolution structure of Grx4, a monothiol glutaredoxin from E. coli.
Componentsmonothiol glutaredoxin ydhD
KeywordsELECTRON TRANSPORT / Mixed alpha/beta fold / Thioredoxin fold
Function / homology
Function and homology information


disulfide oxidoreductase activity / iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / cell redox homeostasis / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / protein homodimerization activity / metal ion binding / cytosol
Similarity search - Function
Monothiol glutaredoxin / Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsFladvad, M. / Bellanda, M. / Fernandes, A.P. / Andresen, C. / Mammi, S. / Holmgren, A. / Vlamis-Gardikas, A. / Sunnerhagen, M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Molecular mapping of functionalities in the solution structure of reduced Grx4, a monothiol glutaredoxin from Escherichia coli.
Authors: Fladvad, M. / Bellanda, M. / Fernandes, A.P. / Mammi, S. / Vlamis-Gardikas, A. / Holmgren, A. / Sunnerhagen, M.
History
DepositionJan 17, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 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: monothiol glutaredoxin ydhD


Theoretical massNumber of molelcules
Total (without water)12,8901
Polymers12,8901
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein monothiol glutaredoxin ydhD / Monothiol glutaredoxin


Mass: 12889.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ydhd / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)grxA-grxB-grxC- / References: UniProt: P0AC69

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
1312D TOCSY
141HNCA
151DQF-COSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 0.8mM Grx4 U,15N,15N-13C; 5mM phopsphate, 125mM KCl
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 125mM KCl / pH: 6.5 / Pressure: ambient / Temperature: 301 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
PROSA3.6Guntertprocessing
XEASY1.4Bartelsdata analysis
ARIA1.2Nilgesstructure solution
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: The structures are based on 2703 NOE-DERIVED distance constraints, 77 J coupling derived dihedral angle restraints, 164 backbone torsion angle restraints derived from chemical shifts
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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