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- PDB-5jyu: NMR structure of pseudo receiver domain of CikA from Thermosynech... -

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Basic information

Entry
Database: PDB / ID: 5jyu
TitleNMR structure of pseudo receiver domain of CikA from Thermosynechococcus elongatus
ComponentsTwo-component sensor histidine kinase
KeywordsSigaling protein / Circadian Clock / Signaling protein
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / rhythmic process / cell division / ATP binding
Similarity search - Function
: / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. ...: / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / CheY-like superfamily / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Circadian input-output histidine kinase CikA
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTseng, R.D. / LiWang, A.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107521 United States
CitationJournal: Science / Year: 2017
Title: Structural basis of the day-night transition in a bacterial circadian clock.
Authors: Tseng, R. / Goularte, N.F. / Chavan, A. / Luu, J. / Cohen, S.E. / Chang, Y.G. / Heisler, J. / Li, S. / Michael, A.K. / Tripathi, S. / Golden, S.S. / LiWang, A. / Partch, C.L.
History
DepositionMay 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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 1.4May 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: Two-component sensor histidine kinase


Theoretical massNumber of molelcules
Total (without water)12,9001
Polymers12,9001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Two-component sensor histidine kinase


Mass: 12899.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: tll0899 / Plasmid: pET28b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8DKG0

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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 HN(COCA)CB
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HBHA(CO)NH
1241isotropic13D H(CCO)NH
1231isotropic13D 1H-15N NOESY
1222isotropic13D 1H-13C NOESY
1212isotropic13D (H)CCH-COSY
1203isotropic13D IPAP-HNCO(CA)
1194anisotropic13D IPAP-HNCO(CA)
1183isotropic13D IPAP-HNCO
1144anisotropic13D IPAP-HNCO
1251isotropic12D 1H-15N HSQC
1262isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 95% H2O/5% D2O20 mM TRIS 100 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)15N13C_sample_H2O95% H2O/5% D2O
solution21500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 99.96% D2O20 mM TRIS 100 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)15N13C_sample_D2O99.96% D2O
gel solution3300 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 90% H2O/10% D2O10 mM TRIS 50 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)RDC_isotropic90% H2O/10% D2O
gel solution4450 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 90% H2O/10% D2O5.16% stretched polyacrylamide gel made with 6 mm diameter 10 mM TRIS 50 mM NaCl 5 mM TCEP 1x midi protease inhibitor (Roche)RDC_aligned90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1500 uMpseudo receiver domain of CikA[U-99% 13C; U-99% 15N]1
1500 uMpseudo receiver domain of CikA[U-99% 13C; U-99% 15N]2
300 uMpseudo receiver domain of CikA[U-99% 13C; U-99% 15N]3
450 uMpseudo receiver domain of CikA[U-99% 13C; U-99% 15N]4
Sample conditionsIonic strength: 0.1 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 25 C

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.39Schwieters, Kuszewski, Tjandra and Clorerefinement
XippGarrett DS, Powers R, Gronenborn AM, Clore GM. J Magn Reson. 2011 Dec;213(2):357-63. doi: 10.1016/j.jmr.2011.09.007. A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams http://spin.niddk.nih.gov/dgarrett/Xipp/xipp.htmlpeak picking
MARSMars - robust automatic backbone assignment of proteins Journal of Biomolecular NMR, 2004, Volume 30, Number 1, Page 11 Young-Sang Jung, Markus Zweckstetterchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIH2.39Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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