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- PDB-1t4z: Solution structure of the N-terminal domain of Synechococcus elon... -

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Basic information

Entry
Database: PDB / ID: 1t4z
TitleSolution structure of the N-terminal domain of Synechococcus elongatus SasA (25-structures ensemble)
ComponentsAdaptive-response sensory-kinase sasA
KeywordsTRANSFERASE / Alpha/Beta protein / Thioredoxin fold
Function / homology
Function and homology information


circadian regulation of translation / histidine kinase / phosphorelay sensor kinase activity / circadian rhythm / ATP binding
Similarity search - Function
Adaptive-response sensory-kinase SasA / KaiB domain / KaiB domain / KaiB / 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 ...Adaptive-response sensory-kinase SasA / KaiB domain / KaiB domain / KaiB / 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. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Adaptive-response sensory kinase SasA
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing, slow refinement in the presence of database potentials
AuthorsVakonakis, I. / Klewer, D.A. / LiWang, A.C.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structure of the N-terminal domain of the circadian clock-associated histidine kinase SasA.
Authors: Vakonakis, I. / Klewer, D.A. / Williams, S.B. / Golden, S.S. / LiWang, A.C.
History
DepositionApr 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adaptive-response sensory-kinase sasA


Theoretical massNumber of molelcules
Total (without water)11,4831
Polymers11,4831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Adaptive-response sensory-kinase sasA


Mass: 11483.250 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: SASA, SARS / Plasmid: pET32a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q06904, Transferases; Transferring phosphorus-containing groups

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C/15N-separated NOESY
1224D 13C-separated NOESY
1333D 15N-separated NOESY
143HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM N-SasA U-15N, 13C, 20mM phosphate buffer pH 7.0, 100mM NaCl, 95% H2O, 5% D2O95% H2O/5% D2O
20.8mM N-SasA U-15N, 13C, 20mM phosphate buffer pH 7.0, 100mM NaCl, 100% D2O100% D2O
30.8mM N-SasA U-15N, 20mM phosphate buffer pH 7.0, 100mM NaCl, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 100 mM NaCl, 20 mM NaPi / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1 Rev. CVarian Assoc.collection
NMRPipe2.1 Rev. 2002.044.17.08Delaglioprocessing
PIPP4.2.6Garrettdata analysis
XPLOR-NIH2.9.1Clore, Kuszewskistructure solution
XPLOR-NIH2.9.1Clore, Kuszewskirefinement
RefinementMethod: distance geometry, simulated annealing, slow refinement in the presence of database potentials
Software ordinal: 1
Details: The structure is based on 2267 restraints, 1764 were NOE, 197 dihedral angles, 71 couplings, 198 chemical shifts and 34 hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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