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- PDB-4tl7: Crystal structure of N-terminal C1 domain of KaiC -

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Basic information

Entry
Database: PDB / ID: 4tl7
TitleCrystal structure of N-terminal C1 domain of KaiC
ComponentsCircadian clock protein kinase KaiC
KeywordsTRANSFERASE / Serine/threonine-protein kinase
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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Circadian clock KaiC, bacteria / : / Circadian clock protein kinase KaiC / : / KaiC domain / KaiC domain profile. / KaiC-like domain / KaiC / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 1.936 Å
AuthorsAbe, J. / Hiyama, T.B. / Mukaiyama, A. / Son, S. / Akiyama, S.
CitationJournal: Science / Year: 2015
Title: Circadian rhythms. Atomic-scale origins of slowness in the cyanobacterial circadian clock.
Authors: Abe, J. / Hiyama, T.B. / Mukaiyama, A. / Son, S. / Mori, T. / Saito, S. / Osako, M. / Wolanin, J. / Yamashita, E. / Kondo, T. / Akiyama, S.
History
DepositionMay 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Jan 29, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
C: Circadian clock protein kinase KaiC
D: Circadian clock protein kinase KaiC
E: Circadian clock protein kinase KaiC
F: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,25330
Polymers170,2756
Non-polymers3,97824
Water13,133729
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23560 Å2
ΔGint-236 kcal/mol
Surface area45590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.165, 108.165, 224.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-418-

HOH

21D-421-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Circadian clock protein kinase KaiC


Mass: 28379.205 Da / Num. of mol.: 6 / Fragment: UNP residues 1-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / Gene: kaiC, Synpcc7942_1216, see0011 / Production host: Escherichia coli (E. coli)
References: UniProt: Q79PF4, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 753 molecules

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: PEG 400 or PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.936→50 Å / Num. obs: 110530 / % possible obs: 97.1 % / Redundancy: 10 % / Net I/σ(I): 48.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.936→45.853 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 5515 5 %
Rwork0.1498 --
obs0.1519 110214 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.936→45.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10791 0 228 729 11748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01911509
X-RAY DIFFRACTIONf_angle_d1.71915638
X-RAY DIFFRACTIONf_dihedral_angle_d14.6454350
X-RAY DIFFRACTIONf_chiral_restr0.11761
X-RAY DIFFRACTIONf_plane_restr0.0091990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9356-1.95760.26521590.19343085X-RAY DIFFRACTION87
1.9576-1.98070.21271800.16883284X-RAY DIFFRACTION93
1.9807-2.00480.20651620.16733354X-RAY DIFFRACTION93
2.0048-2.03020.25571780.16793322X-RAY DIFFRACTION94
2.0302-2.05690.24991880.15833319X-RAY DIFFRACTION93
2.0569-2.08510.23351740.15553352X-RAY DIFFRACTION94
2.0851-2.11490.19161780.14553372X-RAY DIFFRACTION94
2.1149-2.14640.21752020.14963328X-RAY DIFFRACTION95
2.1464-2.180.20741710.15063406X-RAY DIFFRACTION95
2.18-2.21570.17681870.14113385X-RAY DIFFRACTION95
2.2157-2.25390.21411800.14473419X-RAY DIFFRACTION94
2.2539-2.29490.21372090.14273376X-RAY DIFFRACTION96
2.2949-2.3390.20562100.15693420X-RAY DIFFRACTION97
2.339-2.38680.18991780.1523448X-RAY DIFFRACTION97
2.3868-2.43870.20131700.15053537X-RAY DIFFRACTION97
2.4387-2.49540.20881640.15313524X-RAY DIFFRACTION98
2.4954-2.55780.20651840.15543552X-RAY DIFFRACTION98
2.5578-2.6270.22241540.16473585X-RAY DIFFRACTION99
2.627-2.70430.20291880.14823582X-RAY DIFFRACTION99
2.7043-2.79150.21171810.15933582X-RAY DIFFRACTION100
2.7915-2.89130.21481620.15813620X-RAY DIFFRACTION100
2.8913-3.0070.21031940.16473630X-RAY DIFFRACTION100
3.007-3.14380.19711880.15813584X-RAY DIFFRACTION100
3.1438-3.30960.21161900.15833631X-RAY DIFFRACTION100
3.3096-3.51680.19252070.14363603X-RAY DIFFRACTION100
3.5168-3.78830.16231960.13593642X-RAY DIFFRACTION100
3.7883-4.16930.15892030.12693668X-RAY DIFFRACTION100
4.1693-4.7720.13492100.11723635X-RAY DIFFRACTION100
4.772-6.01010.17631800.14793749X-RAY DIFFRACTION100
6.0101-45.86570.19841880.18053705X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -30.135 Å / Origin y: 20.3297 Å / Origin z: -30.114 Å
111213212223313233
T0.1808 Å20.0069 Å20.0031 Å2-0.1233 Å2-0.0235 Å2--0.1678 Å2
L0.3097 °2-0.0242 °2-0.0298 °2-0.4356 °20.0333 °2--0.3572 °2
S0.0188 Å °-0.034 Å °0.1022 Å °0.0235 Å °-0.0182 Å °-0.0089 Å °-0.0862 Å °-0.0319 Å °-0.0004 Å °
Refinement TLS groupSelection details: all

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