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- PDB-1rqv: Spatial model of L7 dimer from E.coli with one hinge region in he... -

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Basic information

Entry
Database: PDB / ID: 1rqv
TitleSpatial model of L7 dimer from E.coli with one hinge region in helical state
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
Single helix bin / 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 ...Single helix bin / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein bL12
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
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
B: 50S ribosomal protein L7/L12


Theoretical massNumber of molelcules
Total (without water)24,3562
Polymers24,3562
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)1 / 100structures with the least restraint violations,target function
RepresentativeModel #1closest to the average

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Components

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


Mass: 12177.960 Da / Num. of mol.: 2 / Fragment: L7 dimer
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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 modeled using NMR and X-Ray structure of protein L7/L12.

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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
Details: The model of L7 dimer with the one unordered, extended hinge region and the second hinge region in helical conformation was calculated using the mean NMR structures of its N- and C-terminal ...Details: The model of L7 dimer with the one unordered, extended hinge region and the second hinge region in helical conformation was calculated using the mean NMR structures of its N- and C-terminal domains and NMR derived constraints obtained for U-15N protein L7, as well as angle constraints for the helical hinge region, which are obtained from X-Ray structure of protein L12 from T.maritima (PDB code 1DD3).
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,target function
Conformers calculated total number: 100 / Conformers submitted total number: 1

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