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- PDB-6twr: Structure of a constitutively active CAT-PRD1 mutant of the antit... -

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Basic information

Entry
Database: PDB / ID: 6twr
TitleStructure of a constitutively active CAT-PRD1 mutant of the antiterminator LicT protein.
ComponentsBeta-glucoside bgl operon antiterminator BglG family
KeywordsRNA BINDING PROTEIN / antitermination protein / Bacillus subtilis / dimeric protein / regulated by the PTS / histidine phosphorylation / activated mutant
Function / homology
Function and homology information


positive regulation of DNA-templated transcription / RNA binding
Similarity search - Function
Transcription antiterminator, conserved site / CAT RNA-binding domain / CAT RNA-binding domain superfamily / CAT RNA binding domain / PRD domain signature. / CAT RNA binding domain / PRD domain / PRD domain / PRD domain superfamily / PRD domain profile.
Similarity search - Domain/homology
Beta-glucoside bgl operon antiterminator BglG family
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDemene, H. / Declerck, N. / Yinshan, Y.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INBS-05 France
Citation
Journal: J.Struct.Biol. / Year: 2021
Title: Resolving the activation mechanism of the D99N antiterminator LicT protein.
Authors: Yang, Y. / Gracy, J. / Declerck, N. / Demene, H.
#1: Journal: Biomol NMR Assign / Year: 2019
Title: NMR chemical shift assignment of a constitutively active fragment of the antitermination protein LicT.
Authors: Yang, Y. / Declerck, N. / Demene, H.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jun 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
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucoside bgl operon antiterminator BglG family
B: Beta-glucoside bgl operon antiterminator BglG family


Theoretical massNumber of molelcules
Total (without water)39,8762
Polymers39,8762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6420 Å2
ΔGint-45 kcal/mol
Surface area16170 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Beta-glucoside bgl operon antiterminator BglG family / PRD domain-containing protein / Transcription antiterminator LicT


Mass: 19937.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: B4122_4365, B4417_2239, ETA10_20555, ETL41_11840, FVD40_12670
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A063XFU4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114isotropic13D 1H-15N TOCSY
124isotropic13D 1H-15N NOESY
236isotropic13D CBCA(CO)NH
245isotropic13D HN(CO)CA
256isotropic13D HNCA
263isotropic12D 1H-13C Filtered NOESY
275isotropic13D HNCO
185isotropic13D HNCA
195isotropic13D CBCA(CO)NH
1105isotropic13D HN(CA)CB
1115isotropic13D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution30.380 mM [U-99% 13C; U-99% 15N] CAT-PRD1 mutant, 200 mM sodium chloride, 10 mM NA TRIS, 0.2 mM EDTA, 0.2 mM Benzamidine, 1 mM DTT, 90% H2O/10% D2Odoubly labelled/non labelled90% H2O/10% D2O
solution41 mM [U-99% 15N] LicT CAT-PRD1 mutant, 200 mM sodium chloride, 0.5 mM EDTA, 0.2 mM Benzamidine, 10 mM TRIS, 1 mM DTT, 90% H2O/10% D2O15N labelled90% H2O/10% D2O15N labelled
solution50.8 mM [U-99% 13C; U-99% 15N] LicT CAT-PRD1 mutant, 200 mM sodium chloride, 10 mM TRIS, 0.5 mM EDTA, 0.2 mM benzamidine, 1 mM DTT, 90% H2O/10% D2O15N/13C -labelled90% H2O/10% D2O
solution60.8 mM [U-99% 13C; U-99% 15N] LicT CAT-PRD1 mutant, 10 mM sodium phosphate, 200 mM NaCl, 0.2 mM EDTA, 0.2 mM DTT, 0.2 mM benzamidine, 90% H2O/10% D2Odoubley labelled acid90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.380 mMCAT-PRD1 mutant[U-99% 13C; U-99% 15N]3
200 mMsodium chloridenatural abundance3
10 mMTRISNA3
0.2 mMEDTAnatural abundance3
0.2 mMBenzamidinenatural abundance3
1 mMDTTnatural abundance3
1 mMLicT CAT-PRD1 mutant[U-99% 15N]4
200 mMsodium chloridenatural abundance4
0.5 mMEDTAnatural abundance4
0.2 mMBenzamidinenatural abundance4
10 mMTRISnatural abundance4
1 mMDTTnatural abundance4
0.8 mMLicT CAT-PRD1 mutant[U-99% 13C; U-99% 15N]5
200 mMsodium chloridenatural abundance5
10 mMTRISnatural abundance5
0.5 mMEDTAnatural abundance5
0.2 mMbenzamidinenatural abundance5
1 mMDTTnatural abundance5
0.8 mMLicT CAT-PRD1 mutant[U-99% 13C; U-99% 15N]6
10 mMsodium phosphatenatural abundance6
200 mMNaClnatural abundance6
0.2 mMEDTAnatural abundance6
0.2 mMDTTnatural abundance6
0.2 mMbenzamidinenatural abundance6
Sample conditions

Ionic strength: 200 mM / PH err: 0.05 / Pressure: 1 atm

Conditions-IDIonic strength errLabelpHTemperature (K)Temperature err
110condition818 308 K0.5
25Condition temp 3006.4 303 K0.1

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.6Bruker Biospincollection
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
Gifa5Delsucdata analysis
CNS3.1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSXplorBrunger, Adams, Clore, Gros, Nilges and Readrefinement
GifaDelsucchemical shift assignment
GifaDelsucpeak picking
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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