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- PDB-5t3y: Solution structure of response regulator protein from Burkholderi... -

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Basic information

Entry
Database: PDB / ID: 5t3y
TitleSolution structure of response regulator protein from Burkholderia multivorans
ComponentsTwo-component system response regulator
KeywordsSIGNALING PROTEIN / response regulator / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyResponse regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesBurkholderia multivorans (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsYang, F. / Lim, Y.-B. / Barnwal, R. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Solution structure of response regulator protein from Burkholderia multivorans
Authors: Yang, F. / Lim, Y.-B. / Barnwal, R. / Varani, G.
History
DepositionAug 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support / Item: _entity.pdbx_number_of_molecules
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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:
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Assembly

Deposited unit
A: Two-component system response regulator


Theoretical massNumber of molelcules
Total (without water)13,0251
Polymers13,0251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7520 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Two-component system response regulator


Mass: 13024.712 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (bacteria) / Gene: WK80_10940 / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D HNCA
161isotropic13D HNCO
171isotropic13D HBHA(CO)NH
182isotropic23D (H)CCH-TOCSY
191isotropic23D 1H-15N NOESY
1101isotropic23D 1H-13C NOESY aliphatic
1111isotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.9 mM [U-13C; U-15N] response regulator protein, 25 mM HEPES, 90% H2O/10% D2O15N13C_sample90% H2O/10% D2O
solution20.9 mM [U-13C; U-15N] response regulator protein, 25 mM HEPES, 100% D2O15N13C_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMresponse regulator protein[U-13C; U-15N]1
25 mMHEPESnatural abundance1
0.9 mMresponse regulator protein[U-13C; U-15N]2
25 mMHEPESnatural abundance2
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameDeveloperClassification
CcpNMRCCPNchemical shift assignment
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: torsion angle dynamics / Software ordinal: 4
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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