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- PDB-6ckq: Solution structure of the Burkholderia thailandensis transcriptio... -

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Basic information

Entry
Database: PDB / ID: 6ckq
TitleSolution structure of the Burkholderia thailandensis transcription antitermination protein NusB (BTH_I1529) - Seattle Structural Genomics Center for Infectious Disease target ButhA.17903.a
ComponentsTranscription antitermination protein NusB
KeywordsTRANSCRIPTION / infectious disease model / transcription antitermnation / NusA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyNusB antitermination factor / NusB/RsmB/TIM44 / NusB family / NusB-like superfamily / transcription antitermination / DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / Transcription antitermination protein NusB
Function and homology information
Biological speciesBurkholderia thailandensis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBuchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HHSN272200700057C United States
CitationJournal: To Be Published
Title: Solution structure of the Burkholderia thailandensis transcription antitermination protein NusB (BTH_I1529).
Authors: Buchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionFeb 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
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 1.3May 15, 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: Transcription antitermination protein NusB


Theoretical massNumber of molelcules
Total (without water)16,3021
Polymers16,3021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The protein was a eluted with a retention time characteristic of a monomer on a size exclusion column (Superdex75). Other spectra properties were consistent with a monomer.
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Transcription antitermination protein NusB / Antitermination factor NusB


Mass: 16301.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264) (bacteria)
Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: nusB, BTH_I1529 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SYC5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CA)CB
1111isotropic13D C(CO)NH
1101isotropic33D 1H-15N NOESY
191isotropic13D 1H-13C NOESY aliphatic
181isotropic13D 1H-13C NOESY aromatic
171isotropic1deuterium exchange
161isotropic12D Deltas

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] NusB, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2O
Label: NusB / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNusB[U-99% 13C; U-99% 15N]1
100 mMsodium chloridenatural abundance1
20 mMTRISnatural abundance1
1 mMDTTnatural abundance1
Sample conditionsIonic strength: 0.12 M / Label: condition_1 / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.4

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXRSVarianVXRS6001
Agilent VXRSAgilentVXRS7502
Agilent VXRSAgilentVXRS8003

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.13Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.5Bhattacharya and Montelionepeak picking
Felix2007Accelrys Software Inc.processing
RefinementMethod: torsion angle dynamics / Software ordinal: 2
Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION ...Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 5% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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