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- PDB-2exd: The solution structure of the C-terminal domain of a nfeD homolog... -

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Basic information

Entry
Database: PDB / ID: 2exd
TitleThe solution structure of the C-terminal domain of a nfeD homolog from Pyrococcus horikoshii
ComponentsnfeD short homolog
KeywordsMEMBRANE PROTEIN / nfeD
Function / homologyNfeD-like, C-terminal domain / NfeD-like C-terminal, partner-binding / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / membrane => GO:0016020 / Beta Barrel / Mainly Beta / : / NfeD domain-containing protein
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodSOLUTION NMR / distance geometry, rigid body restrained molecular dynamics, dihedral angle molecular dynamics
AuthorsKuwahara, Y. / Ohno, A. / Morii, T. / Tochio, H. / Shirakawa, M. / Hiroaki, H.
CitationJournal: Protein Sci. / Year: 2008
Title: The solution structure of the C-terminal domain of NfeD reveals a novel membrane-anchored OB-fold.
Authors: Kuwahara, Y. / Ohno, A. / Morii, T. / Yokoyama, H. / Matsui, I. / Tochio, H. / Shirakawa, M. / Hiroaki, H.
History
DepositionNov 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Experimental preparation
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / 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_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nfeD short homolog


Theoretical massNumber of molelcules
Total (without water)9,2041
Polymers9,2041
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 / 200target function
RepresentativeModel #1closest to the average

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Components

#1: Protein nfeD short homolog


Mass: 9203.565 Da / Num. of mol.: 1 / Fragment: Residues 72-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0471 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codonplus(DE3)-RIL / References: GenBank: 14590384, UniProt: O58204*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
132HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM protein U-15N, 25mM phosphate buffer NA, 300mM NACL, 1mM EDTA, 95% H2O, 5% D2O95% H2O/5% D2O
20.7mM protein U-15N,13C, 25mM phosphate buffer NA, 300mM NACL, 1mM EDTA, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 300mM / pH: 5.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.0.17Peter Guntertstructure solution
XwinNMR3.5Bruker co.collection
NMRPipe2.3F. Delaglioprocessing
Sparky3.106Thomas Goddarddata analysis
CYANA2.0.17Peter Guntertrefinement
RefinementMethod: distance geometry, rigid body restrained molecular dynamics, dihedral angle molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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