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- PDB-4dug: Crystal Structure of Circadian Clock Protein KaiC E318A Mutant -

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Basic information

Entry
Database: PDB / ID: 4dug
TitleCrystal Structure of Circadian Clock Protein KaiC E318A Mutant
Components(Circadian clock protein kinase ...) x 2
KeywordsCIRCADIAN CLOCK PROTEIN / TRANSFERASE / KaiA / KaiB / ATP-binding / biological rhythms / DNA-binding / metal-binding / nucleotide-binding / phosphoprotein / repressor / Serine/threonine-protein kinase / transcription regulation / auto-kinase / phosphorylation
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
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.292 Å
AuthorsEgli, M. / Mori, T. / Pattanayek, R. / Xu, Y. / Qin, X. / Johnson, C.H.
CitationJournal: Biochemistry / Year: 2012
Title: Dephosphorylation of the Core Clock Protein KaiC in the Cyanobacterial KaiABC Circadian Oscillator Proceeds via an ATP Synthase Mechanism.
Authors: Egli, M. / Mori, T. / Pattanayek, R. / Xu, Y. / Qin, X. / Johnson, C.H.
History
DepositionFeb 21, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionMar 14, 2012ID: 3UA2
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)354,96131
Polymers348,4886
Non-polymers6,47325
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56950 Å2
ΔGint-261 kcal/mol
Surface area101370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.714, 135.058, 204.249
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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Circadian clock protein kinase ... , 2 types, 6 molecules ABCEFD

#1: Protein
Circadian clock protein kinase kaiC /


Mass: 58094.719 Da / Num. of mol.: 5 / Mutation: E318A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: kaiC, see0011, Synpcc7942_1216 / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: Q79PF4, non-specific serine/threonine protein kinase
#2: Protein Circadian clock protein kinase kaiC /


Mass: 58014.734 Da / Num. of mol.: 1 / Mutation: E318A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: kaiC, see0011, Synpcc7942_1216 / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: Q79PF4, non-specific serine/threonine protein kinase

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Non-polymers , 4 types, 94 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: sodium formate, glycerol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2010
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.292→112.656 Å / Num. all: 55899 / Num. obs: 50551 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.35 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.5
Reflection shellResolution: 3.292→3.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 1.42 / Num. unique all: 2791 / % possible all: 51.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DVL

3dvl


Resolution: 3.292→30.046 Å / SU ML: 0.4 / Isotropic thermal model: ISOTROPIC / σ(F): 2 / Phase error: 32.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3027 2498 5.06 %
Rwork0.2446 --
obs0.2475 49327 88.41 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.444 Å2 / ksol: 0.279 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-25.1305 Å2-0 Å20 Å2
2--5.7983 Å2-0 Å2
3----30.9288 Å2
Refinement stepCycle: LAST / Resolution: 3.292→30.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23699 0 389 69 24157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01124542
X-RAY DIFFRACTIONf_angle_d0.78133184
X-RAY DIFFRACTIONf_dihedral_angle_d14.3059180
X-RAY DIFFRACTIONf_chiral_restr0.0543697
X-RAY DIFFRACTIONf_plane_restr0.0024236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.292-3.35540.378540.32171189X-RAY DIFFRACTION41
3.3554-3.42380.4154760.30171554X-RAY DIFFRACTION53
3.4238-3.49810.2911900.28471904X-RAY DIFFRACTION65
3.4981-3.57940.37371130.28092257X-RAY DIFFRACTION77
3.5794-3.66870.33211480.28182532X-RAY DIFFRACTION87
3.6687-3.76780.32851610.27892695X-RAY DIFFRACTION93
3.7678-3.87840.34051350.28222787X-RAY DIFFRACTION96
3.8784-4.00330.37821490.27692840X-RAY DIFFRACTION97
4.0033-4.1460.35471620.25992815X-RAY DIFFRACTION97
4.146-4.31160.27091650.23112827X-RAY DIFFRACTION97
4.3116-4.50720.30681530.22292886X-RAY DIFFRACTION98
4.5072-4.7440.25621470.20092855X-RAY DIFFRACTION98
4.744-5.03990.27521440.21962908X-RAY DIFFRACTION98
5.0399-5.42690.3161670.23772896X-RAY DIFFRACTION98
5.4269-5.96920.33051410.28042908X-RAY DIFFRACTION98
5.9692-6.82410.34491520.26942932X-RAY DIFFRACTION98
6.8241-8.56450.24981700.22512960X-RAY DIFFRACTION99
8.5645-30.0470.25971710.21383084X-RAY DIFFRACTION99

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