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- PDB-1pa4: Solution structure of a putative ribosome-binding factor from Myc... -

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Basic information

Entry
Database: PDB / ID: 1pa4
TitleSolution structure of a putative ribosome-binding factor from Mycoplasma pneumoniae (MPN156)
ComponentsProbable ribosome-binding factor A
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ribosome-binding Factor / Distant Homology / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


ribosomal small subunit binding / maturation of SSU-rRNA / cytosol
Similarity search - Function
Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosome-binding factor A
Similarity search - Component
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRubin, S.M. / Pelton, J.G. / Yokota, H. / Kim, R. / Wemmer, D.E. / Berkeley Structural Genomics Center (BSGC)
Citation
Journal: J.STRUCT.FUNCT.GENOM. / Year: 2003
Title: Solution structure of a putative ribosome binding protein from Mycoplasma pneumoniae and comparison to a distant homolog.
Authors: Rubin, S.M. / Pelton, J.G. / Yokota, H. / Kim, R. / Wemmer, D.E.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Solution NMR Structure of Ribosome-binding Factor A (RbfA), a Cold-shock Adaptation Protein from Escherichia Coli
Authors: Huang, Y.J. / Swapna, G.V. / Rajan, P.K. / Ke, H. / Xia, B. / Shukla, K. / Inouye, M. / Montelione, G.T.
History
DepositionMay 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ribosome-binding factor A


Theoretical massNumber of molelcules
Total (without water)13,4141
Polymers13,4141
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)16 / 200Submitted conformers are those with lowest DYANA target functions.
RepresentativeModel #1fewest violations

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Components

#1: Protein Probable ribosome-binding factor A


Mass: 13413.528 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Gene: MPN156 / Plasmid: pSKB3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P75589

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1224D 13C-separated NOESY
1324D 13C/15N-separated NOESY
142HNHA
151H/D Exchange
NMR detailsText: Deposited structures include residues 6-101

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Sample preparation

Details
Solution-IDContentsSolvent system
1~1 mM MPN156 U-15N25mM Sodium Phosphate 1 mM DTT 1 mM EDTA 10% D2O
2~1 mM MPN156 U-15N,U-13C25mM Sodium Phosphate 1 mM DTT 1 mM EDTA 10% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.6 / Pressure: 1 atm / Temperature: 298 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1Delaglioprocessing
NMRView5.0.4Johnsondata analysis
DYANA1.5Guntertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Refinement details can be found in the primary citation above.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: Submitted conformers are those with lowest DYANA target functions.
Conformers calculated total number: 200 / Conformers submitted total number: 16

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