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

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Basic information

Entry
Database: PDB / ID: 8wve
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 / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity ...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 / phosphorylation / 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: 2.729 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)118,29610
Polymers116,1702
Non-polymers2,1268
Water50428
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)354,88730
Polymers348,5096
Non-polymers6,37824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area41250 Å2
ΔGint-200 kcal/mol
Surface area85120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.188, 94.188, 179.168
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: 58084.820 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: 1140 / 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 / Feature type: SUBJECT OF INVESTIGATION / 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.: 28 / 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 Matthews: 1.97 Å3/Da / Density % sol: 37.72 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.729→47.4 Å / Num. obs: 23865 / % possible obs: 99.8 % / Redundancy: 10.7 % / CC1/2: 0.998 / Net I/σ(I): 14.9
Reflection shellResolution: 2.729→2.73 Å / Redundancy: 11 % / Num. unique obs: 2321 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.729→47.138 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.889 / SU B: 29.184 / SU ML: 0.55 / Cross valid method: THROUGHOUT / ESU R Free: 0.504
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns. Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.338 1109 4.647 %RANDOM
Rwork0.28 22755 --
all0.283 ---
obs-23864 99.695 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.884 Å2
Baniso -1Baniso -2Baniso -3
1--5.822 Å2-2.911 Å20 Å2
2---5.822 Å20 Å2
3---18.886 Å2
Refinement stepCycle: LAST / Resolution: 2.729→47.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6407 0 128 28 6563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0116630
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166035
X-RAY DIFFRACTIONr_angle_refined_deg0.6681.6459029
X-RAY DIFFRACTIONr_angle_other_deg0.2721.56313696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.295892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.303548
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.53554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.98810937
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.84410231
X-RAY DIFFRACTIONr_chiral_restr0.0290.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027943
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021549
X-RAY DIFFRACTIONr_nbd_refined0.1880.21384
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.26471
X-RAY DIFFRACTIONr_nbtor_refined0.1780.23289
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23816
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2208
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0890.24
X-RAY DIFFRACTIONr_metal_ion_refined0.1340.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.243
X-RAY DIFFRACTIONr_nbd_other0.2030.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2880.219
X-RAY DIFFRACTIONr_mcbond_it1.6327.2673598
X-RAY DIFFRACTIONr_mcbond_other1.637.2673598
X-RAY DIFFRACTIONr_mcangle_it2.86213.0574480
X-RAY DIFFRACTIONr_mcangle_other2.86313.0574481
X-RAY DIFFRACTIONr_scbond_it1.2016.9313032
X-RAY DIFFRACTIONr_scbond_other1.2016.9313032
X-RAY DIFFRACTIONr_scangle_it2.18212.8974549
X-RAY DIFFRACTIONr_scangle_other2.18112.8964550
X-RAY DIFFRACTIONr_lrange_it4.99672.567205
X-RAY DIFFRACTIONr_lrange_other4.99572.5817203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.729-2.80.461730.40816440.4117680.6160.6797.11540.365
2.8-2.8760.398790.42716220.42517030.8260.71899.88260.385
2.876-2.960.383680.41516080.41416770.7370.75299.94040.37
2.96-3.050.408750.39515510.39516270.7250.81599.93850.348
3.05-3.150.463750.37315000.37715770.7890.85399.87320.337
3.15-3.260.315550.33414630.33315190.9120.88199.93420.294
3.26-3.3820.371560.29314070.29614640.8790.93299.93170.259
3.382-3.520.292640.27113300.27213940.950.9451000.242
3.52-3.6750.289710.25712810.25913540.9390.95599.85230.238
3.675-3.8530.309730.25612140.25912880.9330.96199.92240.243
3.853-4.060.285560.2511850.25112420.9570.9699.91950.241
4.06-4.3050.284600.22311290.22611900.9530.97199.9160.217
4.305-4.5990.255640.21210100.21410750.9640.97499.9070.213
4.599-4.9640.314480.2049950.20810430.9410.9731000.208
4.964-5.4310.353440.2428880.2469320.930.9691000.247
5.431-6.0620.417440.3028200.3078640.950.9571000.299
6.062-6.9810.386360.3027190.3077550.9120.9491000.306
6.981-8.5040.37220.2776290.2816510.9220.9571000.3
8.504-11.8350.31320.2334770.2385090.9510.9751000.255
11.835-47.1380.452140.3422830.3462970.9110.9231000.359

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