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- PDB-1gyz: Bacterial ribosomal protein L20 from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 1gyz
TitleBacterial ribosomal protein L20 from Aquifex aeolicus
Components50S RIBOSOMAL PROTEIN L20
KeywordsRIBOSOMAL PROTEIN / RIBOSOME / PROTEIN SYNTHESIS / TRANSLATIONAL CONTROL / RRNA-BINDING
Function / homology
Function and homology information


cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L20, C-terminal domain / c-terminal domain of poly(a) binding protein / Ribosomal protein L20 signature. / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Large ribosomal subunit protein bL20
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodSOLUTION NMR / HYBRID : DIANA, RESTRAINED SIMULATED ANNEALING
AuthorsRaibaud, S. / Lebars, I. / Bontems, F. / Dardel, F.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: NMR Structure of Bacterial Ribosomal Protein L20: Implications for Ribosome Assembly and Translational Control
Authors: Raibaud, S. / Lebars, I. / Guillier, M. / Chiaruttini, C. / Bontems, F. / Rak, A. / Garber, M. / Allemand, F. / Springer, M. / Dardel, F.
History
DepositionMay 2, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 50S RIBOSOMAL PROTEIN L20


Theoretical massNumber of molelcules
Total (without water)6,7551
Polymers6,7551
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)20 / 100LOWEST DIANA TARGET FUNCTION
RepresentativeModel #7

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Components

#1: Protein 50S RIBOSOMAL PROTEIN L20


Mass: 6754.834 Da / Num. of mol.: 1 / Fragment: RESIDUES 59-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Strain: VF5 / Plasmid: PET11C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PUBS520 / References: UniProt: O67086

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121NOESY-HMQC
131TOCSY-HMQC
141(H)CCH-TOCSY
151NOESY
161DQF-COSY
171HNHA
181HNHB
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED L20. THE FIRST 58 RESIDUES ARE PRESENT IN THE SAMPLE BUT ARE DISORDERED IN SOLUTION

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Sample preparation

Sample conditionsIonic strength: 0.5 / pH: 6.5 / Pressure: 1 atm / Temperature: 318 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.89BRUNGERrefinement
DIANAstructure solution
X-PLORstructure solution
RefinementMethod: HYBRID : DIANA, RESTRAINED SIMULATED ANNEALING / Software ordinal: 1
Details: RESTRAINED SIMUATED ANNEALING FOLLOWED BY A FINAL MINIMIZATION USING THE CHARMM22 FORCEFIELD
NMR ensembleConformer selection criteria: LOWEST DIANA TARGET FUNCTION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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