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- PDB-8wv8: Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC -

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Basic information

Entry
Database: PDB / ID: 8wv8
TitleCrystal Structure of Cyanobacterial Circadian Clock Protein KaiC
ComponentsCircadian clock oscillator protein 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 / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / circadian rhythm / 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 / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / circadian rhythm / 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 nucleoside triphosphate hydrolase
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: 2.93 Å
AuthorsFuruike, Y. / Akiyama, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biophys Physicobio. / Year: 2024
Title: Structure-function relationship of KaiC around dawn.
Authors: Furuike, Y. / Yamashita, E. / Akiyama, S.
History
DepositionOct 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Circadian clock oscillator protein KaiC
B: Circadian clock oscillator protein KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,30010
Polymers116,1742
Non-polymers2,1268
Water28816
1
A: Circadian clock oscillator protein KaiC
B: Circadian clock oscillator protein KaiC
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)354,89930
Polymers348,5216
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 area42490 Å2
ΔGint-239 kcal/mol
Surface area88600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.191, 95.191, 184.086
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Circadian clock oscillator protein KaiC


Mass: 58086.859 Da / Num. of mol.: 2 / Mutation: S431T, T432V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: kaiC / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q79PF4
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 % sol: 40.65 %
Crystal growTemperature: 313 K / Method: evaporation / pH: 7 / Details: sodium/pottasium tartrae, 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: Jul 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.93→49.22 Å / Num. obs: 20257 / % possible obs: 99.7 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 15.8
Reflection shellResolution: 2.93→3.03 Å / Num. unique obs: 1985 / CC1/2: 0.913

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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 / Resolution: 2.93→49.22 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.881 / SU B: 34.63 / SU ML: 0.603 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.586 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3351 939 4.6 %RANDOM
Rwork0.2755 ---
obs0.2783 19328 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.66 Å2 / Biso mean: 71.374 Å2 / Biso min: 30.64 Å2
Baniso -1Baniso -2Baniso -3
1--4.57 Å2-2.28 Å20 Å2
2---4.57 Å2-0 Å2
3---14.82 Å2
Refinement stepCycle: final / Resolution: 2.93→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6510 0 128 16 6654
Biso mean--71.2 48.6 -
Num. residues----911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136740
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176000
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.6399176
X-RAY DIFFRACTIONr_angle_other_deg1.1231.57213700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9445903
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.98520.644295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.46915955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0971549
X-RAY DIFFRACTIONr_chiral_restr0.0290.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027757
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021498
LS refinement shellResolution: 2.93→3.006 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 46 -
Rwork0.445 1427 -
all-1473 -
obs--98 %

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