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- PDB-7dy2: Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC -

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Basic information

Entry
Database: PDB / ID: 7dy2
TitleCrystal Structure of Cyanobacterial Circadian Clock Protein KaiC
Components(Circadian clock protein kinase ...) x 2
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'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 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

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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
G: Circadian clock protein kinase KaiC
H: Circadian clock protein kinase KaiC
K: Circadian clock protein kinase KaiC
L: Circadian clock protein kinase KaiC
I: Circadian clock protein kinase KaiC
J: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)709,33748
Polymers697,75312
Non-polymers11,58436
Water32418
1
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)354,77325
Polymers348,9176
Non-polymers5,85619
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43280 Å2
ΔGint-210 kcal/mol
Surface area93800 Å2
MethodPISA
2
G: Circadian clock protein kinase KaiC
H: Circadian clock protein kinase KaiC
K: Circadian clock protein kinase KaiC
L: Circadian clock protein kinase KaiC
I: Circadian clock protein kinase KaiC
J: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,56423
Polymers348,8376
Non-polymers5,72817
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41690 Å2
ΔGint-207 kcal/mol
Surface area94480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.803, 206.600, 168.383
Angle α, β, γ (deg.)90.000, 94.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Circadian clock protein kinase ... , 2 types, 12 molecules ABEFCDGKLIJH

#1: Protein
Circadian clock protein kinase KaiC /


Mass: 58152.750 Da / Num. of mol.: 11
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: Protein Circadian clock protein kinase KaiC /


Mass: 58072.773 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 54 molecules

#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.31 Å3/Da / Density % sol: 46.65 %
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: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.038→50 Å / Num. obs: 120308 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 15.6
Reflection shellResolution: 3.038→3.15 Å / Rmerge(I) obs: 0.899 / Num. unique obs: 12016

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GBL

2gbl


Resolution: 3.04→49.24 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.837 / SU B: 78.48 / SU ML: 0.624 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.592 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3256 6048 5 %RANDOM
Rwork0.263 ---
obs0.2662 114215 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.94 Å2 / Biso mean: 61.728 Å2 / Biso min: 32 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0 Å20.21 Å2
2---3.22 Å2-0 Å2
3---4.51 Å2
Refinement stepCycle: final / Resolution: 3.04→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38547 0 712 18 39277
Biso mean--69.09 48.64 -
Num. residues----5548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01339914
X-RAY DIFFRACTIONr_bond_other_d0.0020.01832625
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.64254430
X-RAY DIFFRACTIONr_angle_other_deg1.1931.57974751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.31255497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90121.5051747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.087155015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.28315247
X-RAY DIFFRACTIONr_chiral_restr0.030.25830
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0247159
X-RAY DIFFRACTIONr_gen_planes_other0.0020.028842
LS refinement shellResolution: 3.04→3.117 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.416 357 -
Rwork0.374 7466 -
obs--87.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.62760.39090.30551.41750.47430.4404-0.0357-0.1670.0456-0.10610.007-0.03260.00410.11470.02870.22780.0482-0.24590.2668-0.00950.307220.56-12.32991.993
20.78060.5196-0.00461.02990.20190.3447-0.0452-0.3327-0.06840.00240.0003-0.08530.01430.04410.0450.25570.071-0.25210.348-0.01390.2796-2.542-12.55109.845
30.1394-0.15360.07011.27860.43140.27-0.02720.02720.0708-0.1137-0.0228-0.0267-0.06930.00330.05010.312-0.0141-0.30560.16640.00810.3212-7.7419.64255.597
40.35040.07670.121.56870.33020.17640.03130.0030.0438-0.0773-0.0097-0.1349-0.01840.1177-0.02160.1924-0.0253-0.20580.2434-0.0140.283217.773-1.38264.507
50.34040.26580.11490.88320.32820.44510.0185-0.13680.0006-0.0161-0.02390.0174-0.0282-0.04340.00540.19490.0406-0.23310.3132-0.05330.2836-28.492-2.322100.445
60.16980.06170.1791.15610.44770.63180.0263-0.00350.0141-0.0232-0.0601-0.0587-0.0516-0.12220.03380.24020.044-0.28360.1928-0.04970.3625-30.6379.00673.288
70.29380.093-0.24410.61850.29070.4728-0.10890.27330.20930.02310.16440.11540.0486-0.1858-0.05550.2899-0.0403-0.3290.29120.14050.420812.36-24.651155.791
80.7420.57360.28541.11490.4040.3121-0.0089-0.0072-0.00090.01630.01390.0903-0.0422-0.1168-0.0050.19730.0062-0.22220.24950.04380.31699.282-38.001181.05
90.38130.3301-0.07551.39240.1580.3561-0.08450.32420.0111-0.0059-0.0015-0.10840.00640.01270.0860.1924-0.0461-0.20010.43070.02580.250360.423-37.544153.91
100.6461-0.00350.00451.62270.94240.8584-0.1550.51810.21440.06030.07230.15470.06710.06080.08270.2998-0.1347-0.26450.47530.19470.27137.535-24.694141.309
110.74790.63430.28351.58470.39650.1978-0.0031-0.0864-0.10280.1062-0.00780.003-0.029-0.03380.01090.28-0.001-0.23650.18780.01540.247532.678-50.925193.429
120.5060.51990.0951.2530.34320.2598-0.04930.0502-0.1005-0.0120.0127-0.0554-0.02050.05680.03660.241-0.0115-0.25850.2428-0.02170.337758.168-50.997179.556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 498
2X-RAY DIFFRACTION1A602 - 603
3X-RAY DIFFRACTION2B18 - 496
4X-RAY DIFFRACTION2B703
5X-RAY DIFFRACTION3E18 - 497
6X-RAY DIFFRACTION3E604
7X-RAY DIFFRACTION4F17 - 497
8X-RAY DIFFRACTION4F602 - 603
9X-RAY DIFFRACTION5C19 - 498
10X-RAY DIFFRACTION5C602 - 603
11X-RAY DIFFRACTION6D18 - 496
12X-RAY DIFFRACTION6D602 - 603
13X-RAY DIFFRACTION7G18 - 497
14X-RAY DIFFRACTION7G602 - 603
15X-RAY DIFFRACTION8H18 - 499
16X-RAY DIFFRACTION8H602 - 603
17X-RAY DIFFRACTION9K15 - 497
18X-RAY DIFFRACTION9K602 - 603
19X-RAY DIFFRACTION10L18 - 497
20X-RAY DIFFRACTION10L602 - 603
21X-RAY DIFFRACTION11I18 - 498
22X-RAY DIFFRACTION11I602
23X-RAY DIFFRACTION12J17 - 497
24X-RAY DIFFRACTION12J703

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