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- PDB-6tey: Solution Structure of the DNA-binding TubR fragment from Clostrid... -

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Basic information

Entry
Database: PDB / ID: 6tey
TitleSolution Structure of the DNA-binding TubR fragment from Clostridium Botulinum
ComponentsDNA-binding protein TubR
KeywordsDNA BINDING PROTEIN / DNA segregation / partition systems / TubR / winged helix-turn-helix
Function / homologyplasmid partitioning / host cell cytoplasm / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / DNA-binding protein TubR
Function and homology information
Biological speciesClostridium botulinum C phage (virus)
MethodSOLUTION NMR / torsion angle dynamics / molecular dynamics / distance geometry
AuthorsValverde, P. / Canada, F.J. / Jimenez-Barbero, J. / Oliva, M.A.
Funding support Spain, 5items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessFPU14/06147 Spain
Spanish Ministry of Economy and CompetitivenessCTQ2015- 64597-C2 Spain
Spanish Ministry of Economy and CompetitivenessRTI2018-094751-B-C2 Spain
Spanish Ministry of Economy and CompetitivenessBFU2013-47014-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2011-07900 Spain
CitationJournal: To Be Published
Title: Structure of TubR protein fragment from Clostridium Botulinum's phage c-st
Authors: Valverde, P. / Canada, F.J. / Jimenez-Barbero, J. / Oliva, M.A.
History
DepositionNov 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein TubR


Theoretical massNumber of molelcules
Total (without water)9,4341
Polymers9,4341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Also checked by 2D-DOSY NMR
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5800 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150target function
RepresentativeModel #1medoid

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Components

#1: Protein DNA-binding protein TubR / Centromere-binding protein / CBP


Mass: 9434.286 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum C phage (virus) / Gene: tubR, CST190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q331T6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HN(CO)CA
131isotropic13D HNCA
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
161isotropic23D H(CCO)NH
172isotropic22D 1H-1H NOESY
191isotropic12D 1H-15N HSQC
181isotropic22D 1H-13C HSQC
1101isotropic22D 1H-13C HSQC aromatic
1111isotropic23D C(CO)NH
1121isotropic23D (H)CCH-TOCSY
1131isotropic23D (H)CCH-TOCSY
1142isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 225 uM [U-15N] TubR, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM D-10 DTT, 90% H2O/10% D2O
Label: 15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
225 uMTubR[U-15N]2
25 mMpotassium phosphatenatural abundance2
50 mMpotassium chloridenatural abundance2
2 mMDTTD-102
Sample conditionsIonic strength: 80.13 mM / Label: conditions_1 / pH: 6.4 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.05 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001crioprobe
Bruker AVANCEBrukerAVANCE6002PATXI probe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
MolProbityRichardsonrefinement
MolProbityRichardsongeometry optimization
TopSpinBruker Biospinprocessing
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Refinement
MethodSoftware ordinal
torsion angle dynamics5
molecular dynamics9
distance geometry6
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 150 / Conformers submitted total number: 20

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