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- PDB-1d6k: NMR SOLUTION STRUCTURE OF THE 5S RRNA E-LOOP/L25 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1d6k
TitleNMR SOLUTION STRUCTURE OF THE 5S RRNA E-LOOP/L25 COMPLEX
Components
  • 5S RRNA E-LOOP (5SE)
  • RIBOSOMAL PROTEIN L25
KeywordsRIBOSOME / PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


response to radiation / ribosomal large subunit assembly / cytoplasmic translation / 5S rRNA binding / 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
RNA / RNA (> 10) / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsStoldt, M. / Wohnert, J. / Ohlenschlager, O. / Gorlach, M. / Brown, L.R.
CitationJournal: EMBO J. / Year: 1999
Title: The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition.
Authors: Stoldt, M. / Wohnert, J. / Ohlenschlager, O. / Gorlach, M. / Brown, L.R.
History
DepositionOct 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5S RRNA E-LOOP (5SE)
A: RIBOSOMAL PROTEIN L25


Theoretical massNumber of molelcules
Total (without water)22,7382
Polymers22,7382
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)20 / 200target function
RepresentativeModel #2closest to the average

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Components

#1: RNA chain 5S RRNA E-LOOP (5SE)


Mass: 12024.151 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE RNA SEQUENCE WAS SYNTHESIZED VIA IN VITRO TRANSCIPTION (T7 POLYMERASE) OF A PLASMID DNA TEMPLATE.
#2: Protein RIBOSOMAL PROTEIN L25 /


Mass: 10713.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: P68919

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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
2323D F1-13C-FILTERED,F3-EDITED NOESY
5453D 13C-SEPARATED NOESY
3533D 15N-SEPARATED NOESY
3632D NOESY
3732D CPMG NOESY
6863D F1-13C-FILTERED,F3-EDITED NOESY
1913D F1-13C/15N-FILTERED,F3-EDITED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

Details
Solution-IDContents
12MM L25 U-15N,13C/5SE NA; 20MM PHOSPHATE BUFFER; 100MM KCL
22.2MM L25 U-15N,13C/5SE NA; 20MM PHOSPHATE BUFFER; 100MM KCL
31.8MM L25 NA/5SE U-15N; 20MM PHOSPHATE BUFFER; 100MM KCL
41MM L25 U-15N/5SE U-15N; 20MM PHOSPHATE BUFFER; 100MM KCL
51.8MM L25 NA/5SE U-15N,13C; 20MM PHOSPHATE BUFFER; 100MM KCL
61.7MM L25 NA/5SE U-15N,13C; 20MM PHOSPHATE BUFFER; 100MM KCL
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM KCL 7.2 AMBIENT 298 K
2100mM KCL 7.2 AMBIENT 298 K
3100mM KCL 7.2 AMBIENT 298 K
4100mM KCL 7.2 AMBIENT 298 K
5100mM KCL 7.2 AMBIENT 298 K
6100mM KCL 7.2 AMBIENT 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.3Bcollection
XEASY1.3.9BARTELSdata analysis
DYANA1.5GUENTERTstructure solution
OPAL/AMBER942.6LUGINBUEHL/CORNELLrefinement
RefinementMethod: HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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