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- PDB-1m2f: Solution structure of the N-terminal domain of Synechococcus elon... -

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Basic information

Entry
Database: PDB / ID: 1m2f
TitleSolution structure of the N-terminal domain of Synechococcus elongatus KaiA (KaiA135N); Family of 25 structures
ComponentsKaiA
KeywordsCIRCADIAN CLOCK PROTEIN / ALPHA-BETA-ALPHA SANDWICH
Function / homology
Function and homology information


detection of redox state / entrainment of circadian clock / positive regulation of circadian rhythm / circadian rhythm / identical protein binding
Similarity search - Function
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 / CheY-like superfamily ...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 / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Circadian clock oscillator protein KaiA
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodSOLUTION NMR / Distance geometry, Simulated annealing regularization, Simulated annealing refinement
AuthorsWilliams, S.B. / Vakonakis, I. / Golden, S.S. / LiWang, A.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure and Function from the Circadian Clock Protein KaiA of Synechococcus elongatus: A potential Clock Input Mechanism
Authors: Williams, S.B. / Vakonakis, I. / Golden, S.S. / LiWang, A.C.
History
DepositionJun 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KaiA


Theoretical massNumber of molelcules
Total (without water)15,0771
Polymers15,0771
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 #2closest to the average

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Components

#1: Protein KaiA


Mass: 15077.117 Da / Num. of mol.: 1 / Fragment: N-terminal domain (Residues 1-135)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Gene: KaiA / Plasmid: pET32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q79PF6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
1224D 13C/15N-separated NOESY
1334D 13C-separated NOESY
141HNHB
153HAHB
163BRCTCO/BRCTCN
NMR detailsText: Submission corresponds to family of 25-low-energy-structures. The 1H, 15N and 13C chemical shifts of KaiA135N are deposited at the BMRB database (http://www.bmrb.wisc.edu) under the accession number 5031.

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM KaiA135N U-15N; 50mM sodium chloride; 20mM phosphate buffer95% H2O/5% D2O
23mM KaiA135N U-15N,13C; 50mM sodium chloride; 20mM phosphate buffer95% H2O/5% D2O
33mM KaiA135N U-15N,13C; 50mM sodium chloride; 20mM phosphate buffer100% D2O
Sample conditionsIonic strength: 0.17 / pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bVarian Associatescollection
NMRPipe1.8 Rev 2001.030.21.27Delaglioprocessing
PIPP4.2.6Garrettdata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: Distance geometry, Simulated annealing regularization, Simulated annealing refinement
Software ordinal: 1
Details: The structures are based on 2034 restraints: 1816 are NOE-derived distance constraints, 187 dihedral angle restraints, 31 distance restraints from hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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