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- PDB-5c5e: Structure of KaiA dimer in complex with C-terminal KaiC peptide a... -

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Basic information

Entry
Database: PDB / ID: 5c5e
TitleStructure of KaiA dimer in complex with C-terminal KaiC peptide at 2.8 A resolution
Components
  • Circadian clock protein KaiA
  • KaiC C-terminal peptide
KeywordsTRANSCRIPTION / Clock protein KaiA-KaiC complex
Function / homology
Function and homology information


detection of redox state / negative regulation of protein dephosphorylation / regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / positive regulation of circadian rhythm / 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 ...detection of redox state / negative regulation of protein dephosphorylation / regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / positive regulation of circadian rhythm / 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
KaiA/RbsU domain / Circadian clock protein KaiA, N-terminal / Circadian clock protein KaiA, N-terminal domain / KaiA N-terminal domain profile. / Circadian clock protein KaiA / Circadian clock protein KaiA, C-terminal / KaiA C-terminal domain / KaiA C-terminal domain profile. / KaiA / KaiA/RbsU helical domain superfamily ...KaiA/RbsU domain / Circadian clock protein KaiA, N-terminal / Circadian clock protein KaiA, N-terminal domain / KaiA N-terminal domain profile. / Circadian clock protein KaiA / Circadian clock protein KaiA, C-terminal / KaiA C-terminal domain / KaiA C-terminal domain profile. / KaiA / KaiA/RbsU helical domain superfamily / Circadian clock KaiC, bacteria / : / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Circadian clock protein kinase KaiC / : / KaiC domain / KaiC domain profile. / KaiC-like domain / KaiC / CheY-like superfamily / Response regulator / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-52M / Circadian clock oscillator protein KaiC / Circadian clock oscillator protein KaiA
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsPattanayek, R. / Egli, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM073845 United States
CitationJournal: Biochemistry / Year: 2015
Title: Protein-Protein Interactions in the Cyanobacterial Circadian Clock: Structure of KaiA Dimer in Complex with C-Terminal KaiC Peptides at 2.8 angstrom Resolution.
Authors: Pattanayek, R. / Egli, M.
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Circadian clock protein KaiA
G: KaiC C-terminal peptide
B: Circadian clock protein KaiA
H: KaiC C-terminal peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3006
Polymers71,4854
Non-polymers8152
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-53 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.430, 97.430, 124.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Circadian clock protein KaiA /


Mass: 33495.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / Gene: kaiA, Synpcc7942_1218, see0009 / Plasmid: PET32A+ / Production host: ESCHERICHIA COLI / Strain (production host): BL21 / References: UniProt: Q79PF6
#2: Protein/peptide KaiC C-terminal peptide


Mass: 2247.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q79PF4*PLUS
#3: Chemical ChemComp-52M / 2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-5-[(sulfanylcarbonyl)amino]benzoic acid


Mass: 407.396 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H13NO6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 180 mM ammonium sulfate, 85 mM sodium cacodylate pH 6.8, 20% PEG 8000 and 15% glycerol in the reservoir.
PH range: 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.82→46.192 Å / Num. obs: 15075 / % possible obs: 100 % / Redundancy: 22 % / Rmerge(I) obs: 0.1 / Net I/av σ(I): 37.1 / Net I/σ(I): 37.1
Reflection shellResolution: 2.82→2.89 Å / Redundancy: 22.5 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
PHASERphasing
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G86

4g86


Resolution: 2.82→46.192 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3029 732 4.87 %Random selection
Rwork0.2397 ---
obs0.243 15027 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.82→46.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 58 98 5018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035014
X-RAY DIFFRACTIONf_angle_d0.8136795
X-RAY DIFFRACTIONf_dihedral_angle_d15.0591897
X-RAY DIFFRACTIONf_chiral_restr0.025753
X-RAY DIFFRACTIONf_plane_restr0.003893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-3.03770.3651540.26692782X-RAY DIFFRACTION100
3.0377-3.34340.39081180.27892824X-RAY DIFFRACTION100
3.3434-3.8270.30571530.24792813X-RAY DIFFRACTION100
3.827-4.82070.28131430.20912869X-RAY DIFFRACTION100
4.8207-46.19820.27981640.24133007X-RAY DIFFRACTION100

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