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

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Basic information

Entry
Database: PDB / ID: 7dye
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: 2.6 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 21, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,17910
Polymers116,0542
Non-polymers2,1268
Water39622
1
A: Circadian clock protein kinase KaiC
B: Circadian clock protein kinase KaiC
hetero molecules

A: Circadian clock protein kinase KaiC
B: Circadian clock protein kinase KaiC
hetero molecules

A: Circadian clock protein kinase KaiC
B: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,53830
Polymers348,1616
Non-polymers6,37824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area44020 Å2
ΔGint-258 kcal/mol
Surface area89010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.906, 94.906, 276.523
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Circadian clock protein kinase KaiC


Mass: 58026.750 Da / Num. of mol.: 2 / Mutation: S431A, T432A
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.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 313 K / Method: evaporation / pH: 7 / Details: sodium/potassium tartrate, sodium acetate, KCl

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→47.5 Å / Num. obs: 28555 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.5
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.612 / Num. unique obs: 3485

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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: 2GBL

2gbl


Resolution: 2.6→47.5 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.033 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3366 1465 5.1 %RANDOM
Rwork0.2791 ---
obs0.2819 27082 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.57 Å2 / Biso mean: 47.208 Å2 / Biso min: 28.77 Å2
Baniso -1Baniso -2Baniso -3
1--6.27 Å2-3.13 Å20 Å2
2---6.27 Å20 Å2
3---20.33 Å2
Refinement stepCycle: final / Resolution: 2.6→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 128 22 6554
Biso mean--44.85 49.75 -
Num. residues----916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136630
X-RAY DIFFRACTIONr_bond_other_d0.0390.0185737
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.6399031
X-RAY DIFFRACTIONr_angle_other_deg2.5611.57513094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5375908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43820.789279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.24315890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8981545
X-RAY DIFFRACTIONr_chiral_restr0.030.2970
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027727
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021472
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.488 79 -
Rwork0.483 2045 -
all-2124 -
obs--99.81 %

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