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- PDB-1veh: Solution structure of RSGI RUH-018, a NifU-like domain of hirip5 ... -

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Basic information

Entry
Database: PDB / ID: 1veh
TitleSolution structure of RSGI RUH-018, a NifU-like domain of hirip5 protein from mouse cDNA
ComponentsNifU-like protein HIRIP5
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NifU-like / mouse cDNA / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein maturation by [4Fe-4S] cluster transfer / Protein lipoylation / iron-sulfur cluster assembly / 4 iron, 4 sulfur cluster binding / iron ion binding / mitochondrion / cytosol
Similarity search - Function
NIF system FeS cluster assembly, NifU, C-terminal / NifU-like domain / Scaffold protein Nfu/NifU, N-terminal / Scaffold protein Nfu/NifU, N-terminal domain superfamily / Scaffold protein Nfu/NifU N terminal / Scaffold protein Nfu/NifU N terminal / Fe-S cluster assembly (FSCA) / Fe-S cluster assembly domain superfamily / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NFU1 iron-sulfur cluster scaffold homolog, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated anneling torsion angle dynamics
AuthorsOhashi, W. / Hirota, H. / Yamazaki, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution structure of RSGI RUH-018, a NifU-like domain of hirip5 protein from mouse cDNA
Authors: Ohashi, W. / Hirota, H. / Yamazaki, T. / Yokoyama, S.
History
DepositionMar 31, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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: NifU-like protein HIRIP5


Theoretical massNumber of molelcules
Total (without water)9,7891
Polymers9,7891
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 / 100target function
RepresentativeModel #1lowest target function

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Components

#1: Protein NifU-like protein HIRIP5


Mass: 9788.840 Da / Num. of mol.: 1 / Fragment: NifU-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis system / References: UniProt: Q9QZ23

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 1.2mM RSGI RUH-018 U-13C, 15N; 20mM PiNa, 100mM NaCl, 1mM DTT U-2H; 90%H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2.1Delaglioprocessing
NMRView5.0.4Johnsondata analysis
KUJIRA0.8992Kobayashidata analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: simulated anneling torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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