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- PDB-1b75: SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN L25 FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1b75
TitleSOLUTION STRUCTURE OF RIBOSOMAL PROTEIN L25 FROM ESCHERICHIA COLI
ComponentsPROTEIN (50S RIBOSOMAL PROTEIN L25)
KeywordsRNA BINDING PROTEIN / RIBOSOMAL PROTEIN / RNA-BINDING PROTEIN
Function / homology
Function and homology information


response to radiation / ribosomal large subunit assembly / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / structural constituent of ribosome / translation / cytosol / cytoplasm
Similarity search - Function
Ribosomal Protein L25; Chain P / Ribosomal Protein L25; Chain P / Ribosomal protein L25, short-form / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULAT
AuthorsStoldt, M. / Woehnert, J. / Goerlach, M. / Brown, L.R.
CitationJournal: EMBO J. / Year: 1998
Title: The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases.
Authors: Stoldt, M. / Wohnert, J. / Gorlach, M. / Brown, L.R.
History
DepositionJan 27, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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 1.4Dec 27, 2023Group: 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: PROTEIN (50S RIBOSOMAL PROTEIN L25)


Theoretical massNumber of molelcules
Total (without water)10,7131
Polymers10,7131
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100LOWEST TARGET FUNCTION
Representative

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Components

#1: Protein PROTEIN (50S RIBOSOMAL PROTEIN L25)


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P68919

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D/4D HETERONUCLEAR EXPERIMENTS
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N LABELED L25.

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Sample preparation

Sample conditionsIonic strength: 100 mM KCL / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY INOVA / Manufacturer: Varian / Model: UNITY INOVA / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
DYANAGUNTERT,WUTHRICHrefinement
DYANAGUNTERT,WUTHRICHstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULAT / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 100 / Conformers submitted total number: 10

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