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

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Basic information

Entry
Database: PDB / ID: 4tlb
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 / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 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 / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / Rho-dependent protein serine/threonine kinase activity / ribosomal protein S6 kinase activity / histone H2BS14 kinase activity / histone H3T6 kinase activity / histone H3T45 kinase activity / histone H3S10 kinase activity / histone H3T11 kinase activity / AMP-activated protein kinase activity / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / histone H2AS1 kinase activity / non-specific serine/threonine protein kinase / protein serine 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 / 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: 1.983 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_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
Water17,384965
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22720 Å2
ΔGint-194 kcal/mol
Surface area47160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.060, 133.562, 150.835
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: UNP RESIDUES 1-253 / Mutation: S146P
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.: 965 / 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: 2.37 Å3/Da / Density % sol: 48.04 %
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: Dec 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.983→30 Å / Num. obs: 112197 / % possible obs: 99.7 % / Redundancy: 23.7 % / Net I/σ(I): 69

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.983→29.426 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1989 5611 5.01 %
Rwork0.1627 --
obs0.1645 112072 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.983→29.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10712 0 198 965 11875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911322
X-RAY DIFFRACTIONf_angle_d1.15615386
X-RAY DIFFRACTIONf_dihedral_angle_d13.4274276
X-RAY DIFFRACTIONf_chiral_restr0.0471764
X-RAY DIFFRACTIONf_plane_restr0.0061946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9829-2.00540.23681800.18363457X-RAY DIFFRACTION97
2.0054-2.0290.22091850.17183437X-RAY DIFFRACTION98
2.029-2.05380.20261990.16823479X-RAY DIFFRACTION99
2.0538-2.07980.19351720.16763477X-RAY DIFFRACTION99
2.0798-2.10710.21262290.16623490X-RAY DIFFRACTION99
2.1071-2.1360.22861650.16663468X-RAY DIFFRACTION99
2.136-2.16650.21661840.16883542X-RAY DIFFRACTION100
2.1665-2.19880.23631820.17053488X-RAY DIFFRACTION100
2.1988-2.23320.23022000.17013534X-RAY DIFFRACTION100
2.2332-2.26980.20651790.1633502X-RAY DIFFRACTION100
2.2698-2.30890.21471680.16483568X-RAY DIFFRACTION100
2.3089-2.35080.21251960.15923506X-RAY DIFFRACTION100
2.3508-2.3960.20461950.16283529X-RAY DIFFRACTION100
2.396-2.44490.1911880.16283532X-RAY DIFFRACTION100
2.4449-2.49810.22311760.173545X-RAY DIFFRACTION100
2.4981-2.55610.21881700.16853575X-RAY DIFFRACTION100
2.5561-2.620.2011730.16723557X-RAY DIFFRACTION100
2.62-2.69080.23251840.16593530X-RAY DIFFRACTION100
2.6908-2.76990.20571750.16843577X-RAY DIFFRACTION100
2.7699-2.85930.19012240.17743528X-RAY DIFFRACTION100
2.8593-2.96140.24211800.17423564X-RAY DIFFRACTION100
2.9614-3.07980.1831850.17583556X-RAY DIFFRACTION100
3.0798-3.21980.19541860.17043569X-RAY DIFFRACTION100
3.2198-3.38940.20421870.16723581X-RAY DIFFRACTION100
3.3894-3.60140.22261860.16593601X-RAY DIFFRACTION100
3.6014-3.87890.18191790.15353603X-RAY DIFFRACTION100
3.8789-4.26810.15891910.13733600X-RAY DIFFRACTION100
4.2681-4.88330.17112010.12633626X-RAY DIFFRACTION100
4.8833-6.14330.18831890.16573679X-RAY DIFFRACTION100
6.1433-29.4290.17432030.17513761X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.9092 Å / Origin y: 15.7184 Å / Origin z: 17.1028 Å
111213212223313233
T0.1107 Å20.0187 Å2-0.0155 Å2-0.1216 Å20.0266 Å2--0.0985 Å2
L0.3983 °20.1187 °2-0.2466 °2-0.2873 °2-0.0458 °2--0.2934 °2
S-0.0429 Å °-0.0683 Å °-0.0754 Å °0.0423 Å °0.0404 Å °-0.0339 Å °0.0751 Å °0.0324 Å °-0.0037 Å °
Refinement TLS groupSelection details: all

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