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- PDB-7a05: NMR structure of D3-D4 domains of Vibrio vulnificus ribosomal pro... -

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Basic information

Entry
Database: PDB / ID: 7a05
TitleNMR structure of D3-D4 domains of Vibrio vulnificus ribosomal protein S1
Components30S ribosomal protein S1
KeywordsRIBOSOMAL PROTEIN / ribosomal protein S1 domain 3 and domain 4 Vibrio vulnificus OB-fold mRNA binding rS1-D34
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / translation / RNA binding
Similarity search - Function
Ribosomal protein S1 / Ribosomal protein S1-like / RNA-binding domain, S1 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
30S ribosomal protein S1
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodSOLUTION NMR / simulated annealing with torsian angle dynamics / cartesian angle dynamics / molecular dynamics
AuthorsQureshi, N.S. / Matzel, T. / Cetiner, E.C. / Schnieders, S. / Jonker, H.R.A. / Schwalbe, H. / Fuertig, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Collaborative Research Center 902: Molecular principles of RNA-based regulation Germany
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: NMR structure of the Vibrio vulnificus ribosomal protein S1 domains D3 and D4 provides insights into molecular recognition of single-stranded RNAs.
Authors: Qureshi, N.S. / Matzel, T. / Cetiner, E.C. / Schnieders, R. / Jonker, H.R.A. / Schwalbe, H. / Furtig, B.
History
DepositionAug 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Jan 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: 30S ribosomal protein S1


Theoretical massNumber of molelcules
Total (without water)19,3931
Polymers19,3931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: heteronuclear relaxation experiments
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein 30S ribosomal protein S1


Mass: 19393.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ribosomal protein S1 (domain 3 and 4) from Vibrio vulnificus - the initial sequence GAM is introduced by the cloning vector
Source: (gene. exp.) Vibrio vulnificus (bacteria)
Gene: rpsA, CRN34_17730, CRN52_15765, D8T49_21570, JS86_12670
Plasmid: pKMTX / Details (production host): in-house made / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A087IKW3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic52D 1H-15N HSQC
121isotropic53D HNHA
133isotropic53D HNCA
143isotropic53D HN(CO)CA
153isotropic53D HN(CA)CB
163isotropic13D HN(COCA)CB
173isotropic13D HNCO
183isotropic13D HN(CA)CO
193isotropic23D CC(CO)NH
1102isotropic23D HCC(CO)NH
1112isotropic13D (H)CCH-TOCSY
1121isotropic53D 1H-15N NOESY
1132isotropic52D 1H-13C HSQC aliphatic
1142isotropic52D 1H-13C HSQC aromatic
1152isotropic53D 1H-13C NOESY aliphatic
1162isotropic53D 1H-13C NOESY aromatic
1171isotropic12D 1H-15N IPAP-HSQC
1181anisotropic12D 1H-15N IPAP-HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.3 mM [U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT, 95% H2O/5% D2O15N labeled rS1-D34 protein15N95% H2O/5% D2O
solution20.9 mM [U-13C; U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT, 95% H2O/5% D2O13C15N labeled rS1-D34 protein13C15N95% H2O/5% D2O
solution30.7 mM [U-13C; U-15N; 60%-2H] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT, 95% H2O/5% D2O13C15N2H labeled rS1-D34 protein13C15N2H95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMrS1-D34[U-15N]1
25 mMpotassium phosphatenatural abundance1
150 mMpotassium chloridenatural abundance1
5 mMDTTnatural abundance1
0.9 mMrS1-D34[U-13C; U-15N]2
25 mMpotassium phosphatenatural abundance2
150 mMpotassium chloridenatural abundance2
5 mMDTTnatural abundance2
0.7 mMrS1-D34[U-13C; U-15N; 60%-2H]3
25 mMpotassium phosphatenatural abundance3
150 mMpotassium chloridenatural abundance3
5 mMDTTnatural abundance3
Sample conditionsIonic strength: 208 mM / Label: normal / pH: 7.2 / Pressure: ambient mbar / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001cryoprobe
Bruker AVANCEBrukerAVANCE7002cryobrobe
Bruker AVANCEBrukerAVANCE8003cryoprobe
Bruker AVANCEBrukerAVANCE9004cryoprobe
Bruker AVANCEBrukerAVANCE9505cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.x 4.xBruker Biospincollection
TopSpin3.x 4.xBruker Biospinprocessing
Sparky3.114Goddard and Knellerchemical shift assignment
Sparky3.114Goddard and Knellerpeak picking
Sparky3.114Goddard and Knellerdata analysis
CYANA3.xGuntert, Mumenthaler and Wuthrichstructure calculation
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIA1.2 HJLinge, O'Donoghue and Nilgesrefinement
TALOS-NShen and Baxdata analysis
PALESZweckstetter and Baxdata analysis
Refinement
MethodSoftware ordinalDetails
simulated annealing with torsian angle dynamics6structure determination
cartesian angle dynamics7energy minimization
molecular dynamics8refinement in water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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