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- PDB-7dy1: Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC -

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Basic information

Entry
Database: PDB / ID: 7dy1
TitleCrystal Structure of Cyanobacterial Circadian Clock Protein KaiC
Components(Circadian clock protein kinase KaiC) x 2
KeywordsTRANSFERASE / clock protein
Function / homology
Function and homology information


protein serine/threonine/tyrosine kinase activity / circadian rhythm / regulation of circadian rhythm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription ...protein serine/threonine/tyrosine kinase activity / circadian rhythm / regulation of circadian rhythm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
Circadian clock KaiC, bacteria / : / Circadian clock protein kinase KaiC / : / : / KaiC domain / KaiC domain profile. / KaiC-like domain / KaiC / P-loop containing nucleotide triphosphate hydrolases ...Circadian clock KaiC, bacteria / : / Circadian clock protein kinase KaiC / : / : / KaiC domain / KaiC domain profile. / KaiC-like domain / KaiC / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFuruike, Y. / Akiyama, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Regulation mechanisms of the dual ATPase in KaiC.
Authors: Furuike, Y. / Mukaiyama, A. / Koda, S.I. / Simon, D. / Ouyang, D. / Ito-Miwa, K. / Saito, S. / Yamashita, E. / Nishiwaki-Ohkawa, T. / Terauchi, K. / Kondo, T. / Akiyama, S.
History
DepositionJan 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Circadian clock protein kinase KaiC
B: Circadian clock protein kinase KaiC
C: Circadian clock protein kinase KaiC
D: Circadian clock protein kinase KaiC
E: Circadian clock protein kinase KaiC
F: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,87030
Polymers346,4926
Non-polymers6,37824
Water15,079837
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47460 Å2
ΔGint-272 kcal/mol
Surface area84310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.103, 136.492, 190.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Circadian clock protein kinase KaiC


Mass: 57682.008 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: kaiC, tlr0483 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q79V60, non-specific serine/threonine protein kinase
#2: Protein
Circadian clock protein kinase KaiC


Mass: 57761.992 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: kaiC, tlr0483 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q79V60, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 837 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 313 K / Method: evaporation / pH: 5 / Details: Acetatic acid, Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→47.3 Å / Num. obs: 172130 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.989 / Net I/σ(I): 6.9
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 8248 / CC1/2: 0.758

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O0M

4o0m


Resolution: 2.2→47.28 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.748 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2842 8564 5 %RANDOM
Rwork0.2326 ---
obs0.2352 163507 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.1 Å2 / Biso mean: 27.063 Å2 / Biso min: 8.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.97 Å20 Å2
3---1.52 Å2
Refinement stepCycle: final / Resolution: 2.2→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20738 0 384 837 21959
Biso mean--23.55 28.43 -
Num. residues----2731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01321478
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719794
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.64429144
X-RAY DIFFRACTIONr_angle_other_deg1.2511.57145555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6952717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03421.0931043
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.592153507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.90115165
X-RAY DIFFRACTIONr_chiral_restr0.0610.23037
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024721
LS refinement shellResolution: 2.203→2.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 597 -
Rwork0.3 11705 -
all-12302 -
obs--97.62 %

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