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- PDB-5yz8: Crystal Structure of N-terminal C1 domain of KaiC -

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Basic information

Entry
Database: PDB / ID: 5yz8
TitleCrystal Structure of N-terminal C1 domain of KaiC
ComponentsCircadian Clock Protein Kinase KaiC
KeywordsTRANSFERASE / CLOCK PROTEIN
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsMukaiyama, A. / Furuike, Y. / Abe, J. / Akiyama, S.
CitationJournal: Sci Rep / Year: 2018
Title: Conformational rearrangements of the C1 ring in KaiC measure the timing of assembly with KaiB.
Authors: Mukaiyama, A. / Furuike, Y. / Abe, J. / Yamashita, E. / Kondo, T. / Akiyama, S.
History
DepositionDec 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 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 / 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)174,94524
Polymers171,5496
Non-polymers3,39618
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20050 Å2
ΔGint-167 kcal/mol
Surface area46270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.072, 108.072, 224.069
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Circadian Clock Protein Kinase KaiC


Mass: 28591.494 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 1-254 / Mutation: S229W
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 6 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 400, PEG 8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 37912 / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 20.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMAC5.8.0103refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TL7

4tl7


Resolution: 2.81→50 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.845 / SU B: 18.146 / SU ML: 0.359 / Cross valid method: FREE R-VALUE / ESU R Free: 0.453
RfactorNum. reflection% reflection
Rfree0.3 1900 5 %
Rwork0.241 --
obs0.244 35801 99.5 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.06 Å20 Å2
2---0.11 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9640 0 198 37 9875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910116
X-RAY DIFFRACTIONr_bond_other_d0.0030.028956
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.97613793
X-RAY DIFFRACTIONr_angle_other_deg0.914320414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46751327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98822.923390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.308151421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4331569
X-RAY DIFFRACTIONr_chiral_restr0.060.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211619
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022352
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2124.2895341
X-RAY DIFFRACTIONr_mcbond_other1.2124.2895340
X-RAY DIFFRACTIONr_mcangle_it2.1026.4216657
X-RAY DIFFRACTIONr_mcangle_other2.1026.4216658
X-RAY DIFFRACTIONr_scbond_it1.0134.1914775
X-RAY DIFFRACTIONr_scbond_other1.0134.1914776
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7726.2927137
X-RAY DIFFRACTIONr_long_range_B_refined3.70633.67210675
X-RAY DIFFRACTIONr_long_range_B_other3.70433.67710672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.81→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 113 -
Rwork0.298 2535 -
obs--96.33 %

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