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- PDB-2mfi: Domain 1 of E. coli ribosomal protein S1 -

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Basic information

Entry
Database: PDB / ID: 2mfi
TitleDomain 1 of E. coli ribosomal protein S1
Components30S ribosomal protein S1
KeywordsRIBOSOMAL PROTEIN / S1 / ribosome binding / translation initiation
Function / homologyNucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsGiraud, P. / Crechet, J. / Bontems, F. / Uzan, M. / Sizun, C.
CitationJournal: Biomol.Nmr Assign. / Year: 2015
Title: Resonance assignment of the ribosome binding domain of E. coli ribosomal protein S1.
Authors: Giraud, P. / Crechet, J.B. / Uzan, M. / Bontems, F. / Sizun, C.
History
DepositionOct 11, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 30S ribosomal protein S1


Theoretical massNumber of molelcules
Total (without water)10,4301
Polymers10,4301
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)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 30S ribosomal protein S1


Mass: 10429.663 Da / Num. of mol.: 1 / Fragment: UNP residues 11-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpsA, EcDH1_2732, ECDH1ME8569_0862 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: C9QZU1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1523D (H)CCH-TOCSY
1613D HNCO
1713D HN(CA)CO
1833D 1H-15N NOESY
1923D 1H-13C NOESY
11022D 1H-13C HSQC
11123D CCH-TOCSY
11223D (H)CCH-TOCSY aromatic
11322D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM [U-99% 13C; U-99% 15N] S1F1, 25.0 mM potassium phosphate, 200.0 mM potassium chloride, 93% H2O/7% D2O93% H2O/7% D2O
20.2 mM [U-99% 13C; U-99% 15N] S1F1, 25.0 mM potassium phosphate, 200.0 mM potassium chloride, 100% D2O100% D2O
30.5 mM [U-99% 13C; U-99% 15N] S1F1, 25.0 mM potassium phosphate, 200.0 mM potassium chloride, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMS1F1-1[U-99% 13C; U-99% 15N]1
25.0 mMpotassium phosphate-21
200.0 mMpotassium chloride-31
0.2 mMS1F1-4[U-99% 13C; U-99% 15N]2
25.0 mMpotassium phosphate-52
200.0 mMpotassium chloride-62
0.5 mMS1F1-7[U-99% 13C; U-99% 15N]3
25.0 mMpotassium phosphate-83
200.0 mMpotassium chloride-93
Sample conditionsIonic strength: 0.200 / pH: 6.500 / Pressure: 1.000 atm / Temperature: 293.000 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9501
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.2CCPNspectrum display
CcpNmr Analysis2.2CCPNspectrum analysis
TopSpin3.1Brukerspectrum processing
TopSpin3.1Brukerstructure calculation
TopSpin3.1Guntert, Mumenthaler and Wuthrichspectrum processing
TopSpin3.1Guntert, Mumenthaler and Wuthrichstructure calculation
NMRPipeanyDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxspectrum processing
TALOS+anyDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdihedral angles
TopSpin3.1Brukerspectrum processing
TopSpin3.1Brukerstructure calculation
TopSpin3.1Guntert, Mumenthaler and Wuthrichspectrum processing
TopSpin3.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1601 / NOE intraresidue total count: 395 / NOE long range total count: 538 / NOE medium range total count: 185 / NOE sequential total count: 483
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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