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

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Basic information

Entry
Database: PDB / ID: 7dxq
TitleCrystal Structure of Cyanobacterial Circadian Clock Protein KaiC
ComponentsCircadian clock protein kinase KaiC
KeywordsTRANSFERASE / clock protein
Function / homology
Function and homology information


regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / protein serine/threonine/tyrosine kinase activity / circadian rhythm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription ...regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / protein serine/threonine/tyrosine kinase activity / circadian rhythm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFuruike, Y. / Akiyama, S.
CitationJournal: Sci Adv / Year: 2022
Title: Elucidation of master allostery essential for circadian clock oscillation in cyanobacteria.
Authors: Furuike, Y. / Mukaiyama, A. / Ouyang, D. / Ito-Miwa, K. / Simon, D. / Yamashita, E. / Kondo, T. / Akiyama, S.
History
DepositionJan 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 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 1.2Oct 30, 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
E: Circadian clock protein kinase KaiC
F: Circadian clock protein kinase KaiC
C: Circadian clock protein kinase KaiC
D: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,77430
Polymers349,3966
Non-polymers6,37824
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48200 Å2
ΔGint-291 kcal/mol
Surface area84040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.411, 159.874, 207.243
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: 58232.727 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria)
Strain: PCC 7942 / FACHB-805 / Gene: kaiC, Synpcc7942_1216, see0011 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q79PF4, non-specific serine/threonine protein kinase
#2: 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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
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: May 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 75955 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 21.4
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 7451 / CC1/2: 0.751

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GBL

2gbl


Resolution: 2.8→29.96 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.814 / SU B: 22.673 / SU ML: 0.441 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.545 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3176 3284 4.9 %RANDOM
Rwork0.2498 ---
obs0.2532 63354 87.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.83 Å2 / Biso mean: 39.961 Å2 / Biso min: 3.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0 Å20 Å2
2--1.05 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: final / Resolution: 2.8→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20506 0 384 98 20988
Biso mean--37.64 26.14 -
Num. residues----2793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01321275
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719145
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.64128977
X-RAY DIFFRACTIONr_angle_other_deg1.1221.57243809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.69152778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73720.834959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.915153154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.15415152
X-RAY DIFFRACTIONr_chiral_restr0.0310.23077
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0224117
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024691
LS refinement shellResolution: 2.801→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 164 -
Rwork0.329 2564 -
all-2728 -
obs--49.86 %

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