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- PDB-2jnv: Solution structure of C-terminal domain of NifU-like protein from... -

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Basic information

Entry
Database: PDB / ID: 2jnv
TitleSolution structure of C-terminal domain of NifU-like protein from Oryza sativa
ComponentsNifU-like protein 1, chloroplast
KeywordsMETAL TRANSPORT / iron-sulfur cluster binding / program for rice genome reserch / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein maturation by [4Fe-4S] cluster transfer / chloroplast stroma / iron-sulfur cluster assembly / 4 iron, 4 sulfur cluster binding / iron ion binding / mitochondrion
Similarity search - Function
NIF system FeS cluster assembly, NifU, C-terminal / NifU-like domain / 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
NifU-like protein 1, chloroplastic
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, torsion angle dynamics
AuthorsSaio, T. / Ogura, K. / Kumeta, H. / Yokochi, M. / Katoh, S. / Katoh, E. / Inagaki, F. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biochem.(Tokyo) / Year: 2007
Title: The cooperative role of OsCnfU-1A domain I and domain II in the iron sulphur cluster transfer process as revealed by NMR
Authors: Saio, T. / Kumeta, H. / Ogura, K. / Yokochi, M. / Asayama, M. / Katoh, S. / Katoh, E. / Teshima, K. / Inagaki, F.
History
DepositionFeb 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NifU-like protein 1, chloroplast


Theoretical massNumber of molelcules
Total (without water)9,8231
Polymers9,8231
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 energy

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Components

#1: Protein NifU-like protein 1, chloroplast / OsNifu1


Mass: 9823.238 Da / Num. of mol.: 1 / Fragment: residues 73-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: NIFU1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q84LK7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-15N HSQC
2212D 1H-13C HSQC
2313D HNCO
2413D HNCA
2513D HN(CO)CA
2613D HN(CA)CB
2713D CBCA(CO)NH
2813D HN(CA)HA
2913D HBHA(CO)NH
21013D CCH-TOCSY
21113D (H)CCH-TOCSY
21212D (HB)CB(CGCD)HD
21312D (HB)CB(CGCDCE)HE
11412D 1H-15N HSQC
11512D 1H-13C HSQC
11613D 1H-15N NOESY
11713D 1H-13C NOESY

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Sample preparation

DetailsContents: 20 mM sodium phosphate, 150 mM sodium chloride, 0.02 w/v DSS, 10 % D2O, 10 mM DTT, 0.6 mM [U-98% 13C; U-98% 15N] OsNifU1A domain I (73-153), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate1
150 mMsodium chloride1
0.02 w/vDSS1
10 %D2O1
10 mMDTT1
0.6 mMOsNifU1A domain I (73-153)[U-98% 13C; U-98% 15N]1
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11507ambient 298 K
21507.5ambient 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 INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Olivia1.13.1Yokochi, Sekiguchi and Inagakidata analysis
Olivia1.13.1Yokochi, Sekiguchi and Inagakichemical shift assignment
Olivia1.13.1Yokochi, Sekiguchi and Inagakipeak picking
VNMR6.1cVariancollection
NMRPipe23Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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