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- PDB-1k8h: NMR Structure of Small Protein B (SmpB) from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 1k8h
TitleNMR Structure of Small Protein B (SmpB) from Aquifex aeolicus
ComponentsSmall protein B
KeywordsRNA BINDING PROTEIN / SmpB / SsrA associated protein
Function / homology
Function and homology information


trans-translation / RNA binding / cytosol
Similarity search - Function
Small Protein B; Chain: A; / Small protein B / SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
SsrA-binding protein
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDong, G. / Hoffman, D.W.
CitationJournal: EMBO J. / Year: 2002
Title: Structure of small protein B: the protein component of the tmRNA-SmpB system for ribosome rescue.
Authors: Dong, G. / Nowakowski, J. / Hoffman, D.W.
History
DepositionOct 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: 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: Small protein B


Theoretical massNumber of molelcules
Total (without water)15,5231
Polymers15,5231
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)10 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Small protein B / SSRA-BINDING PROTEIN


Mass: 15523.292 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O66640

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
NMR detailsText: This structure was solved using standard 2D and 3D heteronuclear NMR techniques.

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Sample preparation

DetailsContents: 1 mM SmpB / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM / pH: 6 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR softwareName: CNS / Version: 1 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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