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- PDB-6qfp: Solution NMR ensemble for MlbQ at 298K compiled using the CoMAND ... -

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Basic information

Entry
Database: PDB / ID: 6qfp
TitleSolution NMR ensemble for MlbQ at 298K compiled using the CoMAND method
ComponentsPutative lipoprotein
KeywordsSIGNALING PROTEIN / CoMAND method / R-factor refinement
Function / homologyProtein YebY / Protein of unknown function (DUF2511) / Putative lipoprotein
Function and homology information
Biological speciesMicrobispora sp. ATCC PTA-5024 (bacteria)
MethodSOLUTION NMR / R-factor based MD 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 10, 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 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)15,4561
Polymers15,4561
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 area5630 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10000CNH-NOESY based R-factor
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative lipoprotein


Mass: 15456.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbispora sp. ATCC PTA-5024 (bacteria)
Gene: mlbQ, MPTA5024_21425 / Production host: Escherichia coli (E. coli) / References: UniProt: W2EQT0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 3D-CNH NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-99% 13C; U-99% 15N] MlbQ, 20 mM TRIS, 250 mM sodium chloride, 90% H2O/10% D2O
Label: double_labelled / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMlbQ[U-99% 13C; U-99% 15N]1
20 mMTRISnatural abundance1
250 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 240 mM / Label: sample_conditions_1 / pH: 8 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
ShineRiss & Colesstructure calculation
NAMD2.12University of Illinoisstructure calculation
NAMD2.12University of Illinoisrefinement
CoMANDin houserefinement
RefinementMethod: R-factor based MD frame picking / Software ordinal: 6
Details: frames picked from unrestained MD simulations based on overall CNH-NOESY based R-factor
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: CNH-NOESY based R-factor / Conformers calculated total number: 10000 / Conformers submitted total number: 10

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