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- PDB-1rqs: NMR structure of C-terminal domain of ribosomal protein L7 from E.coli -

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Basic information

Entry
Database: PDB / ID: 1rqs
TitleNMR structure of C-terminal domain of ribosomal protein L7 from E.coli
Components50S ribosomal protein L7/L12Ribosome
KeywordsRIBOSOME / protein L7/L12
Function / homology
Function and homology information


ribosome binding / large ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / mRNA binding / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal Protein L30; Chain: A, / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein bL12
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O6 (bacteria)
Escherichia coli O157:H7 (bacteria)
Shigella flexneri (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics in torsion angle space
AuthorsBocharov, E.V. / Sobol, A.G. / Pavlov, K.V. / Korzhnev, D.M. / Jaravine, V.A. / Gudkov, A.T. / Arseniev, A.S.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: From structure and dynamics of protein L7/L12 to molecular switching in ribosome.
Authors: Bocharov, E.V. / Sobol, A.G. / Pavlov, K.V. / Korzhnev, D.M. / Jaravine, V.A. / Gudkov, A.T. / Arseniev, A.S.
History
DepositionDec 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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

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Assembly

Deposited unit
A: 50S ribosomal protein L7/L12


Theoretical massNumber of molelcules
Total (without water)7,5741
Polymers7,5741
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 / 200structures with the least restraint violations,target function
RepresentativeModel #9lowest energy

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Components

#1: Protein 50S ribosomal protein L7/L12 / Ribosome / L8


Mass: 7573.641 Da / Num. of mol.: 1 / Fragment: C-Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli, Escherichia coli O6, Escherichia coli O157:H7, Shigella flexneri
Genus: Escherichia, Escherichia, Escherichia, Shigella / Species: , Escherichia coli, Escherichia coli, / Strain: , O6, O157:H7, / Plasmid: pPR1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 / References: UniProt: P0A7K2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1222D NOESY
1313D 15N-HNHB
14115N-HMQCJ
15315N-JNH MODULATED HSQC
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C90% H2O/10% D2O
21mM L7 dimer U-15N; 50mM phosphate buffer; 99.9% D2O; 30 C99.9% D2O
31mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C; Tobacco virus alignment medium90% H2O/10% D2O
Sample conditionsIonic strength: 0.15 / pH: 6.9 / Pressure: ambient / Temperature: 303 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 spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.3bVARIAN USAcollection
XEASY1.2.11Bartels, C.data analysis
CYANA1.01Guntert, P.structure solution
FANTOM4Schaumann, T.refinement
RefinementMethod: simulated annealing, molecular dynamics in torsion angle space
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,target function
Conformers calculated total number: 200 / Conformers submitted total number: 20

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