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- PDB-1go1: NMR Structure of Ribosomal Protein L30e from Thermococcus celer. -

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Basic information

Entry
Database: PDB / ID: 1go1
TitleNMR Structure of Ribosomal Protein L30e from Thermococcus celer.
Components50S RIBOSOMAL PROTEIN L30E
KeywordsRIBOSOMAL PROTEIN / RNA-BINDING / RIBOSOME / THERMOPHILIC
Function / homology
Function and homology information


cytosolic large ribosomal subunit / structural constituent of ribosome / translation / RNA binding
Similarity search - Function
Ribosomal protein L30/S12 / Ribosomal protein L30e / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like ...Ribosomal protein L30/S12 / Ribosomal protein L30e / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein eL30
Similarity search - Component
Biological speciesTHERMOCOCCUS CELER (archaea)
MethodSOLUTION NMR / SIMULATED ANNEALING USING AMBIGUOUS NOES
Model type detailsMINIMIZED AVERAGE
AuthorsChan, S.-H. / Bycroft, M. / Freund, S.M.V. / Wong, K.-B.
Citation
Journal: Protein Sci. / Year: 2003
Title: Solution Structure and Thermal Stability of Ribosomal Protein L30E from Hyperthermophilic Archaeon Thermococcus Celer
Authors: Wong, K.-B. / Lee, C.-F. / Chan, S.-H. / Leung, T.-Y. / Chen, Y.W. / Bycroft, M.
#1: Journal: Science / Year: 2000
Title: The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 A Resolution
Authors: Ban, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Local Folding Coupled to RNA Binding in the Yeast Ribosomal Protein L30
Authors: Mao, H. / Willamson, J.R.
#3: Journal: Nat.Struct.Biol. / Year: 1999
Title: A Novel Loop-Loop Recognition Motif in the Yeast Ribosomal Protein L30 Autoregulatory RNA Complex
Authors: Mao, H. / White, S.A. / Willamson, J.R.
History
DepositionOct 15, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: 50S RIBOSOMAL PROTEIN L30E


Theoretical massNumber of molelcules
Total (without water)10,9951
Polymers10,9951
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)1 / 400MINIMIZED AVERAGE STRUCTURE OF BEST 10 STRUCTURES WITH THE LOWEST ENERGY
Representative

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Components

#1: Protein 50S RIBOSOMAL PROTEIN L30E


Mass: 10994.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOCOCCUS CELER (archaea) / Plasmid: PRSET-A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P29160

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
13115N-NOESY-HSQC
14113C-NOESY-HSQC
15113C-HSQC-NOESY-HSQC
161HNCA
171HN(CO)CA
181HN(CA)CB
191CBCA(CO)NH
1101(H)CCH-TOCSY
NMR detailsText: MINIMIZED AVERAGE STRUCTURE. THE STRUCTUER WAS DETERMINED USING TRIPLE-RESONANCE NMR EXPERIMENTS ON 13C/ 15N LABELLED SAMPLE

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Sample preparation

DetailsContents: 20MM SODIUM ACETATE, 0.5M NA2SO4
Sample conditionspH: 5.6 / Pressure: AMBIENT / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER ET AL., LINGE ET AL.refinement
NMRPipestructure solution
NMRViewstructure solution
CNSstructure solution
ARIAstructure solution
RefinementMethod: SIMULATED ANNEALING USING AMBIGUOUS NOES / Software ordinal: 1
NMR ensembleConformer selection criteria: MINIMIZED AVERAGE STRUCTURE OF BEST 10 STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 400 / Conformers submitted total number: 1

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