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- PDB-5nb9: Structure of the N-terminal domain of the Escherichia Coli ProQ R... -

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Basic information

Entry
Database: PDB / ID: 5nb9
TitleStructure of the N-terminal domain of the Escherichia Coli ProQ RNA binding protein
ComponentsRNA chaperone ProQ
KeywordsRNA / FinO / ProQ / chaperone
Function / homology
Function and homology information


RNA strand-exchange activity / RNA strand annealing activity / post-transcriptional regulation of gene expression / cytoplasm
Similarity search - Function
RNA chaperone ProQ, C-terminal / ProQ C-terminal domain / RNA chaperone ProQ / ProQ/FinO domain superfamily / ProQ/FINO family / ProQ/FinO domain / ProQ/FINO family
Similarity search - Domain/homology
Biological speciesEscherichia coli O45:K1 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsGonzales, G. / Hardwick, S. / Maslen, S. / Skehel, M. / Holmqvist, E. / Vogel, J. / Bateman, A. / Luisi, B. / Broadhurst, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust094229/Z/10/Z United Kingdom
CitationJournal: RNA / Year: 2017
Title: Structure of the Escherichia coli ProQ RNA-binding protein.
Authors: Gonzalez, G.M. / Hardwick, S.W. / Maslen, S.L. / Skehel, J.M. / Holmqvist, E. / Vogel, J. / Bateman, A. / Luisi, B.F. / Broadhurst, R.W.
History
DepositionMar 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA chaperone ProQ


Theoretical massNumber of molelcules
Total (without water)15,1081
Polymers15,1081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7170 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 50structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA chaperone ProQ


Mass: 15107.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria)
Strain: S88 / ExPEC / Gene: proQ, ECS88_1884 / Plasmid: ProQ-NTD-pET-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B7MBN8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
131isotropic13D 1H-15N TOCSY
242isotropic23D HNCA
252isotropic23D HN(CO)CA
292isotropic23D HN(CA)CB
282isotropic23D CBCA(CO)NH
272isotropic23D HNCO
262isotropic13D (H)CCH-TOCSY
2102isotropic23D 1H-13C NOESY
2112isotropic22D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution120 mM sodium phosphate, 100 mM sodium chloride, 1 mM TCEP, 0.0025 % 3,3,3-trimethylsilylpropionate, 90% H2O/10% D2OAll samples for nuclear magnetic resonance (NMR) spectroscopy were prepared at concentrations of 400-800 uM in buffer containing 20 mM sodium phosphate and 100 mM sodium chloride, supplemented with 1 mM TCEP, protease inhibitor (Roche, 1 tablet/l), 10 % D2O (Sigma) and 0.0025 % 3,3,3- trimethylsilylpropionate (Sigma-Aldrich), in 5 mm Ultra-Imperial grade NMR tubes (Wilmad) to a final volume of 550 uL.15N_sample90% H2O/10% D2O
solution220 mM sodium phosphate, 100 mM sodium chloride, 1 mM TCEP, 0.0025 % 3,3,3-trimethylsilylpropionate, 90% H2O/10% D2OAll samples for nuclear magnetic resonance (NMR) spectroscopy were prepared at concentrations of 400-800 uM in buffer containing 20 mM sodium phosphate and 100 mM sodium chloride, supplemented with 1 mM TCEP, protease inhibitor (Roche, 1 tablet/l), 10 % D2O (Sigma) and 0.0025 % 3,3,3- trimethylsilylpropionate (Sigma-Aldrich), in 5 mm Ultra-Imperial grade NMR tubes (Wilmad) to a final volume of 550 uL.13C_15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
1 mMTCEPnatural abundance1
0.0025 %3,3,3-trimethylsilylpropionatenatural abundance1
20 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
1 mMTCEPnatural abundance2
0.0025 %3,3,3-trimethylsilylpropionatenatural abundance2
Sample conditions

Ionic strength: 150 mM / Ionic strength err: 20 / pH: 6.5 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1

Conditions-IDLabel
115N_sample_1
213C_15N_sample_1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4CCPNdata analysis
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 2
Details: See note above about use of RECOORD refinement protocol
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 17

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