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

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Basic information

Entry
Database: PDB / ID: 4tla
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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 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 1.1Aug 5, 2015Group: Database references
Revision 1.2Jan 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 1.3Mar 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)173,43924
Polymers170,3596
Non-polymers3,08018
Water14,250791
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22530 Å2
ΔGint-171 kcal/mol
Surface area48930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.785, 133.593, 153.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Circadian clock protein kinase KaiC / a4d_1


Mass: 28393.232 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 1-253 / Mutation: S48T
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

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Non-polymers , 5 types, 809 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
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: Oct 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 151590 / % possible obs: 99.8 % / Redundancy: 5.4 % / Net I/σ(I): 26.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.8→38.884 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 7606 5.02 %
Rwork0.1773 --
obs0.1793 151469 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→38.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10716 0 182 791 11689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211323
X-RAY DIFFRACTIONf_angle_d1.36615362
X-RAY DIFFRACTIONf_dihedral_angle_d15.1734288
X-RAY DIFFRACTIONf_chiral_restr0.0691742
X-RAY DIFFRACTIONf_plane_restr0.0071962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8004-1.82090.33152140.28424096X-RAY DIFFRACTION85
1.8209-1.84230.30432590.26884759X-RAY DIFFRACTION100
1.8423-1.86480.2932590.26764778X-RAY DIFFRACTION100
1.8648-1.88840.30892520.2454768X-RAY DIFFRACTION100
1.8884-1.91320.2472210.24874794X-RAY DIFFRACTION100
1.9132-1.93940.28022460.23854816X-RAY DIFFRACTION100
1.9394-1.96710.26632730.21614756X-RAY DIFFRACTION100
1.9671-1.99650.23392900.20414767X-RAY DIFFRACTION100
1.9965-2.02770.2352620.19824741X-RAY DIFFRACTION100
2.0277-2.06090.23762520.20244788X-RAY DIFFRACTION100
2.0609-2.09650.25182200.18984845X-RAY DIFFRACTION100
2.0965-2.13460.24412680.18684758X-RAY DIFFRACTION100
2.1346-2.17560.22992430.18684802X-RAY DIFFRACTION100
2.1756-2.220.21672470.18444821X-RAY DIFFRACTION100
2.22-2.26830.23472670.18424785X-RAY DIFFRACTION100
2.2683-2.32110.22112310.18644804X-RAY DIFFRACTION100
2.3211-2.37910.22612770.17784796X-RAY DIFFRACTION100
2.3791-2.44340.21132640.17834795X-RAY DIFFRACTION100
2.4434-2.51530.23492460.18334847X-RAY DIFFRACTION100
2.5153-2.59650.20542480.17764794X-RAY DIFFRACTION100
2.5965-2.68930.22012500.17374831X-RAY DIFFRACTION100
2.6893-2.79690.21952460.18024841X-RAY DIFFRACTION100
2.7969-2.92410.25592740.18934821X-RAY DIFFRACTION100
2.9241-3.07830.22132600.18574852X-RAY DIFFRACTION100
3.0783-3.2710.21572630.18124845X-RAY DIFFRACTION100
3.271-3.52340.20952670.17194853X-RAY DIFFRACTION100
3.5234-3.87770.2052360.16034898X-RAY DIFFRACTION100
3.8777-4.43810.19482730.1414911X-RAY DIFFRACTION100
4.4381-5.58890.16662550.14124912X-RAY DIFFRACTION99
5.5889-38.89350.21452430.19024989X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -24.807 Å / Origin y: 15.8584 Å / Origin z: -17.5465 Å
111213212223313233
T0.2315 Å2-0.0021 Å2-0.0084 Å2-0.2538 Å2-0.0166 Å2--0.2401 Å2
L0.2993 °2-0.075 °2-0.168 °2-0.2099 °20.005 °2--0.2724 °2
S-0.0224 Å °0.0797 Å °-0.068 Å °-0.0586 Å °0.0143 Å °0.0359 Å °0.0884 Å °-0.0418 Å °0.009 Å °
Refinement TLS groupSelection details: all

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