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- PDB-6qh2: Solution NMR ensemble for a chimeric KH-S1 domain construct of ex... -

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Basic information

Entry
Database: PDB / ID: 6qh2
TitleSolution NMR ensemble for a chimeric KH-S1 domain construct of exosomal polynucleotide phosphrylase at 298K compiled using the CoMAND method
ComponentsPolyribonucleotide nucleotidyltransferase
KeywordsSIGNALING PROTEIN / CoMAND method / R-factor refinement / PHOSPHATASE
Function / homology
Function and homology information


polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / mRNA catabolic process / RNA processing / 3'-5'-RNA exonuclease activity / magnesium ion binding / RNA binding / cytosol
Similarity search - Function
Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / K Homology domain, type 1 / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily ...Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / K Homology domain, type 1 / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Nucleic acid-binding proteins / S1 domain / K Homology domain / K homology RNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / R-factor based frame picking
AuthorsElGamacy, M. / Truffault, V. / Zhu, H. / Coles, M.
CitationJournal: Structure / Year: 2019
Title: Mapping Local Conformational Landscapes of Proteins in Solution.
Authors: ElGamacy, M. / Riss, M. / Zhu, H. / Truffault, V. / Coles, M.
History
DepositionJan 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_nmr_software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_nmr_software.name
Revision 1.2May 15, 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: Polyribonucleotide nucleotidyltransferase


Theoretical massNumber of molelcules
Total (without water)18,3971
Polymers18,3971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9350 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10000back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

#1: Protein Polyribonucleotide nucleotidyltransferase / Polynucleotide phosphorylase / PNPase


Mass: 18396.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain SE11) (bacteria)
Strain: SE11 / Gene: pnp, ECSE_3450 / Production host: Escherichia coli (E. coli)
References: UniProt: B6I1N9, polyribonucleotide nucleotidyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D CBCA(CO)NH
131isotropic13D C(CO)NH
141isotropic13D (H)CCH-TOCSY
151isotropic23D CNH-NOESY

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Sample preparation

DetailsType: solution
Contents: 0.4 mM [U-99% 13C; U-99% 15N] KH-S1, 50 mM potassium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O
Label: double-labelled / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.6 mMKH-S1[U-99% 13C; U-99% 15N]1
50 mMpotassium phosphatenatural abundance1
125 mMsodium chloridenatural abundance1
25 mMHOPES buffernatural abundance2
Sample conditionsIonic strength: 125 mM / Label: conditions_1 / pH: 7.5 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
ShineRiss & Colesstructure calculation
Rosetta3.6Das & Bakerstructure calculation
NAMD2.12University of Illinoisrefinement
CoMANDin houserefinement
RefinementMethod: R-factor based frame picking / Software ordinal: 6
Details: frames picked from unrestrained MD simulations to minimise overall CNH-NOESY based R-Factors
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10000 / Conformers submitted total number: 20

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