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- PDB-9iew: The solution NMR structure of OB domain of ComEC from Moorella gl... -

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Basic information

Entry
Database: PDB / ID: 9iew
TitleThe solution NMR structure of OB domain of ComEC from Moorella glycerini
ComponentsCompetence protein
KeywordsDNA BINDING PROTEIN / OB-fold protein / DNA binding / DNA translocation
Function / homology
Function and homology information


establishment of competence for transformation / plasma membrane
Similarity search - Function
ComEC/Rec2-related protein / Competence protein ComEC/Rec2 / Domain of unknown function DUF4131 / Competence protein / Domain of unknown function (DUF4131) / ComA-like, MBL domain / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Biological speciesMoorella glycerini (bacteria)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsStedman, M.J.M. / Gossert, A.D. / Hospenthal, M.K.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPR00P3_179728 Switzerland
CitationJournal: To Be Published
Title: Molecular interplay between ComEC domains leads to efficient DNA translocation during natural transformation
Authors: Stedman, M.J.M. / Deselaers, S. / Braus, S.A.G. / Wang, D. / Balaguer, M.G. / Gossert, A.D. / Hospenthal, M.K.
History
DepositionFeb 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Competence protein


Theoretical massNumber of molelcules
Total (without water)14,2831
Polymers14,2831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Competence protein


Mass: 14283.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella glycerini (bacteria) / Gene: MGLY_18620 / Plasmid: pOPINS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6I5ZRL0
Has protein modificationN

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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
132isotropic33D (H)CCH-TOCSY
141isotropic23D NOESY combined

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.8 mM [U-13C; U-15N] OB Domain, 50 mM HEPES, 50 mM sodium chloride, 10 % [U-2H] D2O, 90 % H2O, 90% H2O/10% D2OSample for backbone resonance assignment with protonated HEPES. Had to be stored at RT, reducing temperature to 4 C would lead to precipitation.13C-15N OB(76-199)90% H2O/10% D2O
solution20.4 mM [U-13C; U-15N] OB Domain, 50 mM [U-2H] TRIS, 50 mM sodium chloride, 10 % [U-2H] D2O, 90 % H2O, 90% H2O/10% D2OSample for side chain resonance assignment and structure determination with deuterated Tris. Had to be stored at RT, reducing temperature to 4 C would lead to precipitation.13C-15N OB(76-199)90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMOB Domain[U-13C; U-15N]1
50 mMHEPESnatural abundance1
50 mMsodium chloridenatural abundance1
10 %D2O[U-2H]1
90 %H2Onatural abundance1
0.4 mMOB Domain[U-13C; U-15N]2
50 mMTRIS[U-2H]2
50 mMsodium chloridenatural abundance2
10 %D2O[U-2H]2
90 %H2Onatural abundance2
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO7001
Bruker AVANCE III HDBrukerAVANCE III HD9002
Bruker AVANCE III HDBrukerAVANCE III HD6003

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Refinement
MethodSoftware ordinal
simulated annealing3
molecular dynamics4
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 20

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