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

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Basic information

Entry
Database: PDB / ID: 4tld
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 / circadian rhythm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 / circadian rhythm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.949 Å
AuthorsAbe, J. / Hiyama, T.B. / Mukaiyama, A. / Son, S. / Akiyama, S.
CitationJournal: Science / Year: 2015
Title: 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 1.2Jul 29, 2015Group: Database references
Revision 1.3Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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)173,83324
Polymers170,3356
Non-polymers3,49818
Water14,718817
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22800 Å2
ΔGint-197 kcal/mol
Surface area48250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.930, 132.975, 149.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Circadian clock protein kinase KaiC


Mass: 28389.244 Da / Num. of mol.: 6 / Fragment: N-terminal domain, residues 1-253 / Mutation: S157P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus 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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: PEG 400, 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: Feb 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.949→50 Å / Num. obs: 117006 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 23.63

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.949→37.53 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 5854 5.01 %
Rwork0.1753 --
obs0.1769 116908 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.949→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10448 0 198 817 11463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811063
X-RAY DIFFRACTIONf_angle_d1.10115013
X-RAY DIFFRACTIONf_dihedral_angle_d13.8044194
X-RAY DIFFRACTIONf_chiral_restr0.0441710
X-RAY DIFFRACTIONf_plane_restr0.0051909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9486-1.97080.29961930.24213583X-RAY DIFFRACTION98
1.9708-1.9940.2581690.21743689X-RAY DIFFRACTION100
1.994-2.01830.2551970.20963644X-RAY DIFFRACTION100
2.0183-2.04380.26161800.21553679X-RAY DIFFRACTION100
2.0438-2.07070.25891860.20333642X-RAY DIFFRACTION100
2.0707-2.09910.22242020.19493696X-RAY DIFFRACTION100
2.0991-2.12910.24941910.19073635X-RAY DIFFRACTION100
2.1291-2.16080.26531950.18493680X-RAY DIFFRACTION100
2.1608-2.19460.21222060.18183639X-RAY DIFFRACTION100
2.1946-2.23060.23371820.18483692X-RAY DIFFRACTION100
2.2306-2.2690.2241970.17823676X-RAY DIFFRACTION100
2.269-2.31030.23351890.17563681X-RAY DIFFRACTION100
2.3103-2.35470.2261870.17193695X-RAY DIFFRACTION100
2.3547-2.40280.22162140.17173614X-RAY DIFFRACTION100
2.4028-2.4550.2222010.18113692X-RAY DIFFRACTION100
2.455-2.51210.22751990.18513704X-RAY DIFFRACTION100
2.5121-2.57490.25371840.17863697X-RAY DIFFRACTION100
2.5749-2.64450.20092120.17353668X-RAY DIFFRACTION100
2.6445-2.72230.23882000.17173694X-RAY DIFFRACTION100
2.7223-2.81020.19992020.17183684X-RAY DIFFRACTION100
2.8102-2.91060.23611940.17733702X-RAY DIFFRACTION100
2.9106-3.02710.2111740.17793734X-RAY DIFFRACTION100
3.0271-3.16480.20762100.17083707X-RAY DIFFRACTION100
3.1648-3.33150.21081810.1773768X-RAY DIFFRACTION100
3.3315-3.54010.16752110.16513694X-RAY DIFFRACTION100
3.5401-3.81320.19421760.16113771X-RAY DIFFRACTION100
3.8132-4.19650.16312080.1573749X-RAY DIFFRACTION100
4.1965-4.80260.16861990.14063780X-RAY DIFFRACTION100
4.8026-6.04670.18922010.17773815X-RAY DIFFRACTION100
6.0467-37.53660.21792140.19733950X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -24.8933 Å / Origin y: 15.5356 Å / Origin z: -16.932 Å
111213212223313233
T0.1664 Å2-0.0157 Å2-0.0201 Å2-0.1832 Å2-0.0284 Å2--0.1504 Å2
L0.3946 °2-0.0736 °2-0.2473 °2-0.2896 °20.0458 °2--0.2975 °2
S-0.0437 Å °0.0813 Å °-0.0528 Å °-0.0265 Å °0.0507 Å °0.0362 Å °0.0735 Å °-0.0289 Å °-0.0096 Å °
Refinement TLS groupSelection details: all

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