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

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Basic information

Entry
Database: PDB / ID: 4tle
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.936 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)173,87024
Polymers170,3726
Non-polymers3,49818
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22490 Å2
ΔGint-190 kcal/mol
Surface area48170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.927, 133.322, 151.057
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: 28395.271 Da / Num. of mol.: 6 / Fragment: N-terminal domain, residues 1-253 / Mutation: S157C
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 / Chloride


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 / Water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
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: Jun 28, 2013
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: 119433 / % possible obs: 99.5 % / Redundancy: 5.3 % / Net I/σ(I): 29

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.936→42.603 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 6002 5.03 %
Rwork0.1885 --
obs0.1905 119305 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.936→42.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10384 0 198 567 11149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111097
X-RAY DIFFRACTIONf_angle_d1.24615044
X-RAY DIFFRACTIONf_dihedral_angle_d14.3524198
X-RAY DIFFRACTIONf_chiral_restr0.0531710
X-RAY DIFFRACTIONf_plane_restr0.0061911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.936-1.9580.27821540.24193122X-RAY DIFFRACTION82
1.958-1.9810.26282350.22773690X-RAY DIFFRACTION99
1.981-2.00520.28431940.22863763X-RAY DIFFRACTION99
2.0052-2.03060.28261940.22433744X-RAY DIFFRACTION99
2.0306-2.05730.27611860.22693787X-RAY DIFFRACTION99
2.0573-2.08550.2622210.21143730X-RAY DIFFRACTION100
2.0855-2.11530.24732190.20273733X-RAY DIFFRACTION100
2.1153-2.14680.25842100.19783772X-RAY DIFFRACTION100
2.1468-2.18040.25311940.19563729X-RAY DIFFRACTION100
2.1804-2.21610.22071890.19483851X-RAY DIFFRACTION100
2.2161-2.25430.23892250.19793714X-RAY DIFFRACTION100
2.2543-2.29530.25761850.19023801X-RAY DIFFRACTION100
2.2953-2.33950.24241810.1923815X-RAY DIFFRACTION100
2.3395-2.38720.26661860.1923777X-RAY DIFFRACTION100
2.3872-2.43910.21732120.18953785X-RAY DIFFRACTION100
2.4391-2.49580.2612080.20083779X-RAY DIFFRACTION100
2.4958-2.55830.24421910.19673809X-RAY DIFFRACTION100
2.5583-2.62740.21481850.19153796X-RAY DIFFRACTION100
2.6274-2.70470.25522190.19453791X-RAY DIFFRACTION100
2.7047-2.7920.23261660.19863844X-RAY DIFFRACTION100
2.792-2.89180.26482170.2013829X-RAY DIFFRACTION100
2.8918-3.00750.24782070.20413779X-RAY DIFFRACTION100
3.0075-3.14440.25412000.19123837X-RAY DIFFRACTION100
3.1444-3.31010.2432010.20643822X-RAY DIFFRACTION100
3.3101-3.51740.2412000.18573856X-RAY DIFFRACTION100
3.5174-3.78880.19822210.17783834X-RAY DIFFRACTION100
3.7888-4.16980.18861910.16523882X-RAY DIFFRACTION100
4.1698-4.77250.17541980.14163880X-RAY DIFFRACTION100
4.7725-6.01010.21682140.17123927X-RAY DIFFRACTION100
6.0101-42.61340.21841990.21273825X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 24.3269 Å / Origin y: 15.686 Å / Origin z: 16.9092 Å
111213212223313233
T0.1805 Å20.0157 Å2-0.0325 Å2-0.2038 Å20.0228 Å2--0.186 Å2
L0.4353 °20.0865 °2-0.2956 °2-0.3882 °2-0.066 °2--0.3798 °2
S-0.0426 Å °-0.0943 Å °-0.0669 Å °0.0414 Å °0.056 Å °-0.0503 Å °0.103 Å °0.0323 Å °-0.0167 Å °
Refinement TLS groupSelection details: all

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