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- PDB-1wlo: Solution structure of the hypothetical protein from thermus therm... -

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Basic information

Entry
Database: PDB / ID: 1wlo
TitleSolution structure of the hypothetical protein from thermus thermophilus HB8
ComponentssufE protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyFe-S metabolism associated domain, SufE-like / Fe-S metabolism associated domain / Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / Alpha-Beta Complex / Alpha Beta / Iron-sulfur cluster biosynthesis protein SufE
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Solution structure of the hypothetical protein from thermus thermophilus HB8
Authors: Hayashi, F. / Yokoyama, S.
History
DepositionJun 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sufE protein


Theoretical massNumber of molelcules
Total (without water)15,1801
Polymers15,1801
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, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein sufE protein / hypothetical protein TTC0409


Mass: 15179.624 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SK87

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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

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Sample preparation

DetailsContents: 0.72mM protein U-15N, 13C; 20mM phosphate buffer NA; 150mM NaCl; 0.02% NaN3; 1mM DTT
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 170mM / pH: 7.2 / Pressure: ambient / 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 spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.902Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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