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- PDB-3dvl: Crystal Structure of Full Length Circadian Clock Protein KaiC wit... -

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Basic information

Entry
Database: PDB / ID: 3dvl
TitleCrystal Structure of Full Length Circadian Clock Protein KaiC with Correct Geometry at Phosphorylation Sites
ComponentsCircadian clock protein kinase kaiC
KeywordsCIRCADIAN CLOCK PROTEIN / Transferase / HOMOHEXAMER / CIRCADIAN / KAIA / KAIB / KAIC / HEXAMER / KINASE / ATP-binding / Biological rhythms / DNA-binding / Magnesium / Metal-binding / Nucleotide-binding / Phosphoprotein / Repressor / Serine/threonine-protein kinase / Transcription / Transcription regulation
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 / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / refinement / Resolution: 2.8 Å
AuthorsPattanayek, R. / Egli, M.
CitationJournal: To be Published
Title: Crystal Structure of Full Length Circadian Clock Protein KaiC with Correct Geometry at Phosphorylation Sites
Authors: Pattanayek, R. / Williams, D.R. / Pattanayek, S. / Xu, Y. / Mori, T. / Johnson, C.H. / Stewart, P.L. / Egli, M.
History
DepositionJul 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)355,62824
Polymers349,3966
Non-polymers6,23218
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53030 Å2
ΔGint-181 kcal/mol
Surface area97590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.873, 135.576, 204.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S).

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Components

#1: Protein
Circadian clock protein kinase kaiC


Mass: 58232.727 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC7942 / Gene: kaiC / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: SODIUM FORMATE, GLYCEROL, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11.25
SYNCHROTRONAPS 5ID-B21
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJun 1, 2003
MARRESEARCH2CCDJul 10, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(220)MADMx-ray1
2SI(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.251
211
ReflectionResolution: 2.8→30 Å / Num. all: 87750 / Num. obs: 87750 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.6
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
RAVEmodel building
GLRFphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RAVEphasing
RefinementMethod to determine structure: refinement
Starting model: PDB entry 2GBL

2gbl


Resolution: 2.8→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 4041 -random
Rwork0.2392 ---
all-79746 --
obs-75705 89.6 %-
Displacement parametersBiso mean: 73.676 Å2
Baniso -1Baniso -2Baniso -3
1--12.208 Å20 Å20 Å2
2---3.339 Å20 Å2
3---15.548 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23426 0 378 66 23870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d2.1166
X-RAY DIFFRACTIONc_bond_d0.021694

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