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- PDB-1fox: NMR STRUCTURE OF L11-C76, THE C-TERMINAL DOMAIN OF 50S RIBOSOMAL ... -

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Basic information

Entry
Database: PDB / ID: 1fox
TitleNMR STRUCTURE OF L11-C76, THE C-TERMINAL DOMAIN OF 50S RIBOSOMAL PROTEIN L11, 33 STRUCTURES
ComponentsL11-C76
KeywordsRIBOSOMAL PROTEIN / RNA-BINDING DOMAIN / L11-C76 / ALPHA-HELICAL PROTEIN / HOMEODOMAIN FOLD
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 / DGSA
AuthorsMarkus, M.A. / Hinck, A.P. / Huang, S. / Draper, D.E. / Torchia, D.A.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA.
Authors: Markus, M.A. / Hinck, A.P. / Huang, S. / Draper, D.E. / Torchia, D.A.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: The RNA Binding Domain of Ribosomal Protein L11 is Structurally Similar to Homeodomains
Authors: Xing, Y. / Guha Thakurta, D. / Draper, D.E.
#2: Journal: Biochemistry / Year: 1996
Title: Cooperative Interactions of RNA and Thiostrepton Antibiotic with Two Domains of Ribosomal Protein L11
Authors: Xing, Y. / Draper, D.E.
History
DepositionSep 13, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 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: L11-C76


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)33 / 50NO NOE VIOLATIONS OVER 0.3 A, NO ANGLE VIOLATIONS OVER 5 DEG
Representative

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Components

#1: Protein L11-C76


Mass: 8152.554 Da / Num. of mol.: 1
Fragment: CARBOXYL-TERMINAL DOMAIN OF PROTEIN L11, RESIDUES THR 59 TO ASP 133
Mutation: INS(MET1)
Source method: isolated from a genetically manipulated source
Details: BINDS SPECIFICALLY TO RNA
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cell line: BL21 / Plasmid: DERIVED FROM PET11A / 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N HSQC
12113C HSQC
131HN(CA)CB
141CBCA(CO)NH
151HCACO
161C(CO)NH
171H(CCO)NH
181(H)CCH-TOCSY
191HMBC
1101HNHA
1111HNHB
1121HCACB-COSY
1131(13CO)SED CT HSQC
1141(15N) SED CT HSQC
1151(13C-13C) LRC
1161(13C-1H) LRC
NMR detailsText: BUFFER: 10 MM K2HPO4, 25 MM KCL, 2MM MGCL2

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Sample preparation

Sample conditionspH: 6.1 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DMXBrukerDMX5002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DGSA / Software ordinal: 1
NMR ensembleConformer selection criteria: NO NOE VIOLATIONS OVER 0.3 A, NO ANGLE VIOLATIONS OVER 5 DEG
Conformers calculated total number: 50 / Conformers submitted total number: 33

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