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- PDB-1ib8: SOLUTION STRUCTURE AND FUNCTION OF A CONSERVED PROTEIN SP14.3 ENC... -

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Basic information

Entry
Database: PDB / ID: 1ib8
TitleSOLUTION STRUCTURE AND FUNCTION OF A CONSERVED PROTEIN SP14.3 ENCODED BY AN ESSENTIAL STREPTOCOCCUS PNEUMONIAE GENE
ComponentsCONSERVED PROTEIN SP14.3
KeywordsNUCLEIC ACID BINDING PROTEIN / RIBOSOMAL PROTEIN / ESSENTIAL GENE / STRUCTURAL GENOMICS
Function / homology
Function and homology information


ribosomal small subunit biogenesis / cytoplasm
Similarity search - Function
Ribosome maturation factor RimP, C-terminal domain / RimP-like superfamily, N-terminal / Ribosome maturation factor RimP / Ribosome maturation factor RimP, N-terminal / Ribosome maturation factor RimP, C-terminal / RimP, N-terminal domain superfamily / Ribosome maturation factor RimP, C-terminal domain superfamily / RimP N-terminal domain / RimP C-terminal SH3 domain / GMP Synthetase; Chain A, domain 3 ...Ribosome maturation factor RimP, C-terminal domain / RimP-like superfamily, N-terminal / Ribosome maturation factor RimP / Ribosome maturation factor RimP, N-terminal / Ribosome maturation factor RimP, C-terminal / RimP, N-terminal domain superfamily / Ribosome maturation factor RimP, C-terminal domain superfamily / RimP N-terminal domain / RimP C-terminal SH3 domain / GMP Synthetase; Chain A, domain 3 / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ribosome maturation factor RimP
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing protocol
Model type detailsminimized average
AuthorsYu, L. / Gunasekera, A.H. / Mack, J. / Olejniczak, E.T. / Chovan, L.E. / Ruan, X. / Towne, D.L. / Lerner, C.G. / Fesik, S.W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: SOLUTION STRUCTURE AND FUNCTION OF A CONSERVED PROTEIN SP14.3 ENCODED BY AN ESSENTIAL STREPTOCOCCUS PNEUMONIAE GENE
Authors: Yu, L. / Gunasekera, A.H. / Mack, J. / Olejniczak, E.T. / Chovan, L.E. / Ruan, X. / Towne, D.L. / Lerner, C.G. / Fesik, S.W.
History
DepositionMar 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 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: CONSERVED PROTEIN SP14.3


Theoretical massNumber of molelcules
Total (without water)18,1931
Polymers18,1931
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)1 / -
Representativeminimized average structure

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Components

#1: Protein CONSERVED PROTEIN SP14.3


Mass: 18192.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ESSENTIAL GENE / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q97S61

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY, TOCSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1 mM SP14.3 15N-labeled, 15N,13C-labeled, and 15N,13C,2H-labeled with selectively protonated methyl groups. 50 mM BisTris HCl, pH 6.5, 50 mM ammonium sulphate.
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.5 / Pressure: ambient / 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 DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
in-house softwaredata analysis
CNX software2000 ParallelBrunger et al.structure solution
CNX2000BRUNGERrefinement
RefinementMethod: distance geometry, simulated annealing protocol / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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