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- PDB-4tl6: Crystal structure of N-terminal domain of KaiC -

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Basic information

Entry
Database: PDB / ID: 4tl6
TitleCrystal structure of N-terminal 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.763 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 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,83512
Polymers85,1383
Non-polymers1,6989
Water5,711317
1
A: Circadian clock protein kinase KaiC
B: Circadian clock protein kinase KaiC
C: Circadian clock protein kinase KaiC
hetero molecules

A: Circadian clock protein kinase KaiC
B: Circadian clock protein kinase KaiC
C: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,67124
Polymers170,2756
Non-polymers3,39618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area22830 Å2
ΔGint-164 kcal/mol
Surface area47170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.823, 81.057, 95.640
Angle α, β, γ (deg.)90.00, 132.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Circadian clock protein kinase KaiC /


Mass: 28379.205 Da / Num. of mol.: 3 / 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
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
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 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.762→50 Å / Num. obs: 74255 / % possible obs: 100 % / Redundancy: 3.8 % / Net I/σ(I): 22.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GBL

2gbl


Resolution: 1.763→38.12 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.75 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 3736 5.04 %
Rwork0.1686 --
obs0.1705 74154 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.763→38.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5292 0 99 317 5708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145603
X-RAY DIFFRACTIONf_angle_d1.4787597
X-RAY DIFFRACTIONf_dihedral_angle_d13.6492124
X-RAY DIFFRACTIONf_chiral_restr0.076864
X-RAY DIFFRACTIONf_plane_restr0.007965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7626-1.78490.29831320.24882433X-RAY DIFFRACTION94
1.7849-1.80840.27011450.22882601X-RAY DIFFRACTION100
1.8084-1.83310.25221280.232629X-RAY DIFFRACTION100
1.8331-1.85930.27491560.22482522X-RAY DIFFRACTION100
1.8593-1.88710.29751300.21812657X-RAY DIFFRACTION100
1.8871-1.91660.24291540.20232596X-RAY DIFFRACTION100
1.9166-1.9480.21081260.18452593X-RAY DIFFRACTION100
1.948-1.98160.22041220.17092641X-RAY DIFFRACTION100
1.9816-2.01760.22291490.17432607X-RAY DIFFRACTION100
2.0176-2.05640.24361280.17392568X-RAY DIFFRACTION100
2.0564-2.09840.21541260.16672638X-RAY DIFFRACTION100
2.0984-2.1440.211260.16132604X-RAY DIFFRACTION100
2.144-2.19390.20781230.16312656X-RAY DIFFRACTION100
2.1939-2.24870.22431330.16642627X-RAY DIFFRACTION100
2.2487-2.30950.22531390.16822586X-RAY DIFFRACTION100
2.3095-2.37750.19321350.16652630X-RAY DIFFRACTION100
2.3775-2.45420.17951490.15742605X-RAY DIFFRACTION100
2.4542-2.54190.21591440.16222619X-RAY DIFFRACTION100
2.5419-2.64370.19351340.15692566X-RAY DIFFRACTION100
2.6437-2.76390.2141490.15512607X-RAY DIFFRACTION100
2.7639-2.90960.22571410.16242640X-RAY DIFFRACTION100
2.9096-3.09180.1871420.16092597X-RAY DIFFRACTION100
3.0918-3.33040.18751610.16692594X-RAY DIFFRACTION100
3.3304-3.66530.19651310.15622662X-RAY DIFFRACTION100
3.6653-4.19510.2021310.15752633X-RAY DIFFRACTION100
4.1951-5.28320.16551480.14752633X-RAY DIFFRACTION100
5.2832-38.12930.2211540.19082674X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 1.7346 Å / Origin y: -0.3084 Å / Origin z: 20.4549 Å
111213212223313233
T0.1494 Å2-0.006 Å2-0.0021 Å2-0.0694 Å20.005 Å2--0.1335 Å2
L0.5419 °2-0.0798 °2-0.0306 °2-0.1197 °20.0192 °2--0.6048 °2
S0.0169 Å °-0.021 Å °0.0563 Å °0.0295 Å °0.0067 Å °-0.0045 Å °-0.0875 Å °-0.0089 Å °-0.0212 Å °
Refinement TLS groupSelection details: all

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