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- PDB-1q6a: Solution Structure of the C-terminal Domain of Thermosynechococcu... -

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Basic information

Entry
Database: PDB / ID: 1q6a
TitleSolution Structure of the C-terminal Domain of Thermosynechococcus elongatus KaiA (ThKaiA180C); Averaged Minimized Structure
ComponentsCircadian clock protein KaiA homolog
KeywordsCIRCADIAN CLOCK PROTEIN / All alpha-helix protein / Homodimer
Function / homology
Function and homology information


circadian rhythm / identical protein binding
Similarity search - Function
KaiA/RbsU domain / Circadian clock protein KaiA, N-terminal / Circadian clock protein KaiA, N-terminal domain / KaiA N-terminal domain profile. / Circadian clock protein KaiA / Circadian clock protein KaiA, C-terminal / KaiA C-terminal domain / KaiA C-terminal domain profile. / KaiA / KaiA/RbsU helical domain superfamily ...KaiA/RbsU domain / Circadian clock protein KaiA, N-terminal / Circadian clock protein KaiA, N-terminal domain / KaiA N-terminal domain profile. / Circadian clock protein KaiA / Circadian clock protein KaiA, C-terminal / KaiA C-terminal domain / KaiA C-terminal domain profile. / KaiA / KaiA/RbsU helical domain superfamily / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / CheY-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Circadian clock oscillator protein KaiA / Circadian clock oscillator protein KaiA
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodSOLUTION NMR / Distance geometry, Simulated Annealing, Radius-of-gyration, Carbon chemical shift, conformational database potential refinement
Model type detailsminimized average
AuthorsVakonakis, I. / Sun, J. / Holzenburg, A. / Golden, S.S. / LiWang, A.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: NMR structure of the KaiC-interacting C-terminal domain of KaiA, a circadian clock protein: Implications for KaiA-KaiC interaction
Authors: Vakonakis, I. / Sun, J. / Wu, T. / Holzenburg, A. / Golden, S.S. / LiWang, A.C.
History
DepositionAug 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Circadian clock protein KaiA homolog
B: Circadian clock protein KaiA homolog


Theoretical massNumber of molelcules
Total (without water)25,2032
Polymers25,2032
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein Circadian clock protein KaiA homolog /


Mass: 12601.585 Da / Num. of mol.: 2 / Fragment: C-terminal domain (ThKaiA180C)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: KaiA / Plasmid: pET-32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RR35, UniProt: Q79V62*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1234D 13C-separated NOESY
1343D 13C-edited, 12C filtered NOESY
143HACAHB
151HNHB
163BRCTCO/CN
172CBCA(CO)NH
182CBCANH
NMR detailsText: This is the oxidized form of the protein. A disulfide bond connects residue C96 of each monomeric unit.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM ThKaiA180C U-15N, 20 mM NaCl, 20 mM phosphate buffer, 95% H2O, 5% D2O95% H2O/5% D2O
21.3 mM ThKaiA180C U-15N,U-13C, 20 mM NaCl, 20 mM phosphate buffer, 95% H2O, 5% D2O95% H2O/5% D2O
31.3 mM ThKaiA180C U-15N,U-13C, 20 mM NaCl, 20 mM phosphate buffer, 100% D2O100% D2O
41 mM ThKaiA180C U-15N,U-13C, 1 mM ThKaiA180C NA-N,NA-C, 20 mM NaCl, 20 mM phosphate buffer, 100% D2O100% D2O
Sample conditionsIonic strength: 20 mM NaCl, 20 mM NaPi / pH: 7.0 / Pressure: ambient / Temperature: 323 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
NMRPipe2.1 Rev 2002.044.17.08Delaglioprocessing
PIPP4.2.6Garrettdata analysis
XPLOR-NIH2.9.1Clorestructure solution
VNMR6.1 Rev. CVarian Assoc.collection
XPLOR-NIH2.9.1Clorerefinement
RefinementMethod: Distance geometry, Simulated Annealing, Radius-of-gyration, Carbon chemical shift, conformational database potential refinement
Software ordinal: 1
Details: The structure is based on 2207 restraints of which 1740 are NOE restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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