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- PDB-2fow: THE RNA BINDING DOMAIN OF RIBOSOMAL PROTEIN L11: THREE-DIMENSIONA... -

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Basic information

Entry
Database: PDB / ID: 2fow
TitleTHE RNA BINDING DOMAIN OF RIBOSOMAL PROTEIN L11: THREE-DIMENSIONAL STRUCTURE OF THE RNA-BOUND FORM OF THE PROTEIN, NMR, 26 STRUCTURES
ComponentsRIBOSOMAL PROTEIN L11
KeywordsRIBOSOME / PROTEIN:RNA / THIOSTREPTON
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex
Similarity search - Function
Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily ...Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodSOLUTION NMR / SUBSTRUCTURE DISTANCE GEOMETRY, SIMULATING ANNEALING
AuthorsHinck, A.P. / Markus, M.A. / Huang, S. / Grzesiek, S. / Kustanovich, I. / Draper, D.E. / Torchia, D.A.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: The RNA binding domain of ribosomal protein L11: three-dimensional structure of the RNA-bound form of the protein and its interaction with 23 S rRNA.
Authors: Hinck, A.P. / Markus, M.A. / Huang, S. / Grzesiek, S. / Kustonovich, I. / Draper, D.E. / Torchia, D.A.
History
DepositionMay 26, 1997Processing site: BNL
Revision 1.0Nov 26, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 29, 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: RIBOSOMAL PROTEIN L11


Theoretical massNumber of molelcules
Total (without water)8,1531
Polymers8,1531
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)26 / 50NOE VIOL < 0.3 ANGSTROMS DIHEDRAL VIOL < 3 DEGREES; 3JHNHA COUPLING VIOLATED < 1.5 HZ
Representative

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Components

#1: Protein RIBOSOMAL PROTEIN L11


Mass: 8152.554 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, 75 RESIDUES / Mutation: F1M
Source method: isolated from a genetically manipulated source
Details: STRUCTURE OF THE PROTEIN IN THIS ENTRY WAS DETERMINED AS A 1\:1 COMPLEX WITH ITS TARGET RNA OF 58 NUCLEOTIDES, BASES 1051 - 1108 OF THE E. COLI SEQUENCE
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P56210

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 6.1 / Temperature: 320 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX 500BrukerDMX 5005001
Bruker DMX 600BrukerDMX 6006002

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.8BRUNGERrefinement
X-PLOR3.8structure solution
RefinementMethod: SUBSTRUCTURE DISTANCE GEOMETRY, SIMULATING ANNEALING
Software ordinal: 1
Details: SUBSTRUCTURE DISTANCE GEOMETRY/ SIMULATED ANNEALING PROTOCOL
NMR ensembleConformer selection criteria: NOE VIOL < 0.3 ANGSTROMS DIHEDRAL VIOL < 3 DEGREES; 3JHNHA COUPLING VIOLATED < 1.5 HZ
Conformers calculated total number: 50 / Conformers submitted total number: 26

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