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- PDB-2kic: n-NafY. N-terminal domain of NafY -

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Basic information

Entry
Database: PDB / ID: 2kic
Titlen-NafY. N-terminal domain of NafY
ComponentsNitrogenase gamma subunit
KeywordsPROTEIN BINDING / METAL TRANSPORT / n-NafY / Nitrogenase Gamma Subunit
Function / homology
Function and homology information


metal cluster binding / nitrogen fixation
Similarity search - Function
Dinitrogenase iron-molybdenum cofactor, N-terminal / Nitrogen fixation protein NifX / Dinitrogenase iron-molybdenum cofactor, N-terminal / NifX-like domain / Dinitrogenase iron-molybdenum cofactor, N-terminal domain superfamily / Dinitrogenase iron-molybdenum cofactor, N-terminal / : / Dinitrogenase iron-molybdenum cofactor biosynthesis / Dinitrogenase iron-molybdenum cofactor biosynthesis superfamily / Dinitrogenase iron-molybdenum cofactor ...Dinitrogenase iron-molybdenum cofactor, N-terminal / Nitrogen fixation protein NifX / Dinitrogenase iron-molybdenum cofactor, N-terminal / NifX-like domain / Dinitrogenase iron-molybdenum cofactor, N-terminal domain superfamily / Dinitrogenase iron-molybdenum cofactor, N-terminal / : / Dinitrogenase iron-molybdenum cofactor biosynthesis / Dinitrogenase iron-molybdenum cofactor biosynthesis superfamily / Dinitrogenase iron-molybdenum cofactor / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nitrogenase gamma subunit
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPhillips, A.H. / Hernandez, J.A. / Erbil, K. / Pelton, J.G. / Wemmer, D.E. / Rubio, L.M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Biological activity and solution structure of the apo-dinitrogenase binding domain of NafY
Authors: Phillips, A.H. / Hernandez, J.A. / Erbil, K. / Pelton, J.G. / Wemmer, D.E. / Rubio, L.M.
History
DepositionMay 1, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogenase gamma subunit


Theoretical massNumber of molelcules
Total (without water)10,4801
Polymers10,4801
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nitrogenase gamma subunit


Mass: 10479.966 Da / Num. of mol.: 1 / Fragment: Residues 1-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nafY / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9F5X9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] n-NafY, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: n-NafY / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 150 / pH: 7.3 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 900 MHz

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Processing

NMR softwareName: X-PLOR / Developer: Brunger A.T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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