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- PDB-7v3x: Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC -

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Basic information

Entry
Database: PDB / ID: 7v3x
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 / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 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 / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine 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'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFuruike, Y. / Akiyama, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
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
DepositionAug 11, 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 23, 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

Downloads & links

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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
N: Circadian clock protein kinase KaiC
O: Circadian clock protein kinase KaiC
R: Circadian clock protein kinase KaiC
M: Circadian clock protein kinase KaiC
P: Circadian clock protein kinase KaiC
Q: Circadian clock protein kinase KaiC
T: Circadian clock protein kinase KaiC
U: Circadian clock protein kinase KaiC
X: Circadian clock protein kinase KaiC
S: Circadian clock protein kinase KaiC
V: Circadian clock protein kinase KaiC
W: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,421,525108
Polymers1,396,54624
Non-polymers24,98084
Water1,65792
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)355,61430
Polymers349,2366
Non-polymers6,37824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)355,61430
Polymers349,2366
Non-polymers6,37824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
N: Circadian clock protein kinase KaiC
O: Circadian clock protein kinase KaiC
R: Circadian clock protein kinase KaiC
M: Circadian clock protein kinase KaiC
P: Circadian clock protein kinase KaiC
Q: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,30127
Polymers349,0766
Non-polymers6,22521
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
T: Circadian clock protein kinase KaiC
U: Circadian clock protein kinase KaiC
X: Circadian clock protein kinase KaiC
S: Circadian clock protein kinase KaiC
V: Circadian clock protein kinase KaiC
W: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,99621
Polymers348,9966
Non-polymers5,99915
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.492, 205.803, 186.177
Angle α, β, γ (deg.)90.000, 115.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21G
12B
22H
13C
23I
14D
24J
15E
25K
16F
26L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A15 - 500
2112G15 - 500
1122B15 - 500
2122H15 - 500
1132C15 - 500
2132I15 - 500
1142D15 - 500
2142J15 - 500
1152E15 - 500
2152K15 - 500
1162F15 - 500
2162L15 - 500

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999959, -0.003361, -0.008377), (0.003366, 0.999994, 0.000659), (0.008375, -0.000687, 0.999965)40.890079, -0.47553, -84.373573
3given(1), (1), (1)
4given(0.999937, -0.003682, -0.010632), (0.003681, 0.999993, -0.000157), (0.010632, 0.000118, 0.999943)41.302399, -0.23215, -84.343323
5given(1), (1), (1)
6given(0.999976, -0.002328, -0.006566), (0.002315, 0.999995, -0.001976), (0.006571, 0.001961, 0.999977)40.770248, 0.09572, -84.270409
7given(1), (1), (1)
8given(0.999951, -0.001544, -0.00981), (0.001559, 0.999997, 0.001597), (0.009807, -0.001612, 0.999951)41.30769, -0.50273, -84.47271
9given(1), (1), (1)
10given(0.999918, -0.001404, -0.012744), (0.001469, 0.999986, 0.005089), (0.012736, -0.005107, 0.999906)41.84737, -1.20114, -84.562263
11given(1), (1), (1)
12given(0.999969, -0.003403, -0.007156), (0.003406, 0.999994, 0.000431), (0.007155, -0.000455, 0.999974)40.687462, -0.41081, -84.458801

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Components

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Circadian clock protein kinase ... , 2 types, 24 molecules ABGHNRMPTXSVWEFCDKLIJOQU

#1: Protein
Circadian clock protein kinase KaiC


Mass: 58152.750 Da / Num. of mol.: 13
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: 58232.727 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

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Non-polymers , 4 types, 176 molecules

#3: Chemical...
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.6 %
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: Oct 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 228464 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 13.8
Reflection shellResolution: 3.1→3.15 Å / Rmerge(I) obs: 0.744 / Num. unique obs: 11426

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Processing

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

2gbl


Resolution: 3.1→49.22 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.831 / SU B: 74.258 / SU ML: 0.585 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.678 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3397 10614 4.9 %RANDOM
Rwork0.2745 ---
obs0.2777 204692 93.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.36 Å2 / Biso mean: 48.304 Å2 / Biso min: 9.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0 Å2-0.61 Å2
2--0.26 Å2-0 Å2
3---0.8 Å2
Refinement stepCycle: final / Resolution: 3.1→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms77135 0 1512 92 78739
Biso mean--54.04 30.49 -
Num. residues----11050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01379891
X-RAY DIFFRACTIONr_bond_other_d0.010.01866805
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.642108936
X-RAY DIFFRACTIONr_angle_other_deg1.3021.578152844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.769510923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60521.2553410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.0531510317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.13315503
X-RAY DIFFRACTIONr_chiral_restr0.040.211717
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0293360
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0217525
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3747MEDIUM POSITIONAL0.270.5
1A2736TIGHT THERMAL2.860.5
1A3747MEDIUM THERMAL2.682
2B3665MEDIUM POSITIONAL0.290.5
2B2753TIGHT THERMAL2.130.5
2B3665MEDIUM THERMAL2.142
3C3603MEDIUM POSITIONAL0.30.5
3C2771TIGHT THERMAL2.550.5
3C3603MEDIUM THERMAL2.512
4D3648MEDIUM POSITIONAL0.270.5
4D2752TIGHT THERMAL2.250.5
4D3648MEDIUM THERMAL2.12
5E3667MEDIUM POSITIONAL0.270.5
5E2771TIGHT THERMAL1.630.5
5E3667MEDIUM THERMAL1.532
6F3652MEDIUM POSITIONAL0.270.5
6F2759TIGHT THERMAL1.820.5
6F3652MEDIUM THERMAL1.812
LS refinement shellResolution: 3.1→3.175 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.38 512 -
Rwork0.342 9722 -
obs--60.6 %
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)
10.21930.20360.05361.0134-0.01440.06120.0180.01410.0255-0.00050.02430.0402-0.0355-0.0479-0.04230.15370.0210.08730.07220.02590.157127.36510.71773.594
20.19140.10950.031.0299-0.09010.13160.04680.0458-0.0004-0.1034-0.0376-0.018-0.0006-0.0363-0.00920.19710.0250.0840.07250.00080.088246.418-0.21654.123
30.43070.3550.02310.5681-0.09410.1696-0.0249-0.03690.02790.02210.01950.03830.00330.04550.00540.1867-0.00890.0790.0653-0.03550.110459.617-1.072111.468
40.32340.18410.09350.73210.1210.1167-0.0009-0.03890.00540.0008-0.00680.0294-0.0756-0.04640.00770.21050.01310.11750.0305-0.00630.126934.14610.34102.241
50.25380.1197-0.23210.6013-0.23130.25530.0524-0.02010.0127-0.0806-0.03590.00540.00690.0484-0.01650.19130.01230.09680.0612-0.040.117472.319-11.2963.146
60.24730.2497-0.15030.6535-0.19870.2070.0036-0.01290.0002-0.01880.0425-0.0140.03890.0894-0.04610.12790.01650.06150.0802-0.05340.1678.51-12.61892.081
70.17930.11360.07540.70790.07160.04720.0177-0.0242-0.0047-0.00850.01340.0649-0.0346-0.0251-0.03120.13790.01570.07060.06030.04110.1786-12.2310.893158.069
80.14940.1070.04250.913-0.04320.04270.05350.0319-0.0092-0.0765-0.02870.0522-0.02080.0025-0.02480.2009-0.01190.06790.07210.00350.09816.553-0.195138.409
90.43760.34180.00770.5726-0.10060.1171-0.0529-0.04410.02850.06270.06790.0233-0.00790.0156-0.0150.17940.02240.07680.0834-0.03710.097320.316-0.819195.849
100.35940.25920.11160.74130.05740.0746-0.0163-0.04950.0170.01130.03440.0204-0.0606-0.0553-0.01810.17740.03220.11520.05730.00470.1284-4.94810.962186.7
110.2560.1557-0.22340.7636-0.18440.21970.0625-0.02960.0174-0.097-0.0399-0.0164-0.01150.0247-0.02260.1763-0.00080.08680.0453-0.0230.132532.321-11.827147.339
120.22970.1795-0.160.7785-0.17640.1431-0.022-0.01530.011-0.01560.0718-0.07030.02980.0346-0.04980.12080.01150.05340.0818-0.05590.159338.908-12.342176.154
130.4290.3846-0.02470.69820.14590.17340.07880.1647-0.01540.05640.0314-0.0497-0.0653-0.18-0.11020.04830.10040.0610.24820.11490.131484.264-24.375153.802
140.29480.306-0.07690.454-0.00290.19470.0730.0174-0.01630.0895-0.02310.0181-0.0666-0.1725-0.04990.06460.05140.07920.17720.04830.156885.471-25.055182.918
150.3230.1193-0.24570.9209-0.04880.21550.0510.0588-0.0217-0.0106-0.1207-0.03760.0047-0.04040.06970.09160.0010.04890.10910.0630.1335127.832-50.327150.471
160.1840.204-0.03311.4031-0.0180.18640.08560.11280.0201-0.0035-0.087-0.0323-0.0086-0.16450.00140.06650.0640.0460.21790.02020.0579105.233-36.361137.412
170.4270.2279-0.07070.5874-0.18920.31750.0032-0.02740.01220.0432-0.0451-0.03610.016-0.04640.04190.0943-0.05840.04770.14180.03560.0808108.935-37.733195.936
180.35830.144-0.19270.7174-0.07120.18590.02830.03950.0310.0847-0.0644-0.02730.0493-0.00240.03610.1088-0.05470.00070.09970.07240.1434129.548-50.827180.008
190.0788-0.0028-0.120.01450.00920.19650.08520.20260.06340.0155-0.0173-0.016-0.1047-0.3669-0.06790.09260.15590.04610.76840.08810.1063123.681-24.9369.689
200.73670.5376-0.1280.88130.09860.18790.11280.0668-0.04590.0902-0.0829-0.0877-0.0305-0.2683-0.02990.04860.03840.02940.5010.05550.0518127.001-25.48799.444
210.3280.0818-0.170.61070.07890.15140.13320.1082-0.01070.0369-0.1444-0.1004-0.012-0.16980.01120.123-0.04470.03110.30990.03390.0524168.008-51.83665.973
220.34820.180.15770.37890.0890.38030.13810.04710.0296-0.0404-0.1927-0.091-0.001-0.32440.05460.10410.16740.04460.55270.04320.0471144.926-37.76953.168
230.24260.0068-0.18380.6518-0.04650.1555-0.07070.0941-0.03070.12280.0514-0.05910.0701-0.12940.01930.1379-0.1060.03730.26270.030.0743150.31-38.505111.575
240.33470.1861-0.04360.81810.03350.07120.08770.01430.10320.133-0.058-0.08960.0855-0.1137-0.02960.1634-0.1612-0.0030.20240.04110.0719170.801-50.62694.877
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 497
2X-RAY DIFFRACTION2B17 - 497
3X-RAY DIFFRACTION3E17 - 497
4X-RAY DIFFRACTION4F15 - 497
5X-RAY DIFFRACTION5C16 - 497
6X-RAY DIFFRACTION6D17 - 497
7X-RAY DIFFRACTION7G17 - 497
8X-RAY DIFFRACTION8H17 - 497
9X-RAY DIFFRACTION9K17 - 498
10X-RAY DIFFRACTION10L15 - 497
11X-RAY DIFFRACTION11I16 - 498
12X-RAY DIFFRACTION12J18 - 497
13X-RAY DIFFRACTION13N18 - 498
14X-RAY DIFFRACTION14O16 - 497
15X-RAY DIFFRACTION14O703
16X-RAY DIFFRACTION15R18 - 497
17X-RAY DIFFRACTION16M17 - 497
18X-RAY DIFFRACTION16M703
19X-RAY DIFFRACTION17P18 - 497
20X-RAY DIFFRACTION18Q18 - 497
21X-RAY DIFFRACTION19T18 - 497
22X-RAY DIFFRACTION19T703
23X-RAY DIFFRACTION20U20 - 497
24X-RAY DIFFRACTION20U703
25X-RAY DIFFRACTION21X17 - 497
26X-RAY DIFFRACTION22S18 - 497
27X-RAY DIFFRACTION23V18 - 497
28X-RAY DIFFRACTION23V703
29X-RAY DIFFRACTION24W18 - 498

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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