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- PDB-5jwr: Crystal structure of foldswitch-stabilized KaiB in complex with t... -

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Basic information

Entry
Database: PDB / ID: 5jwr
TitleCrystal structure of foldswitch-stabilized KaiB in complex with the N-terminal CI domain of KaiC and a dimer of KaiA C-terminal domains from Thermosynechococcus elongatus
Components
  • Circadian clock protein KaiA
  • Circadian clock protein KaiB
  • Circadian clock protein kinase KaiC
KeywordsTranscription Regulator / foldswitch
Function / homology
Function and homology information


negative regulation of phosphorylation / protein serine/threonine/tyrosine kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / regulation of circadian rhythm / circadian rhythm / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity ...negative regulation of phosphorylation / protein serine/threonine/tyrosine kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / regulation of circadian rhythm / circadian rhythm / kinase activity / protein autophosphorylation / 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 protein KaiA, N-terminal / Circadian clock protein KaiA, N-terminal domain / KaiA N-terminal domain profile. / Circadian clock protein KaiA / Circadian clock protein KaiB / Circadian clock protein KaiA, C-terminal / KaiA C-terminal domain / KaiA C-terminal domain profile. / KaiA / Circadian clock protein KaiB-like ...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 KaiB / Circadian clock protein KaiA, C-terminal / KaiA C-terminal domain / KaiA C-terminal domain profile. / KaiA / Circadian clock protein KaiB-like / KaiA/RbsU helical domain superfamily / KaiB domain / KaiB domain / KaiB / Circadian clock KaiC, bacteria / : / Circadian clock protein kinase KaiC / : / KaiC domain / KaiC domain profile. / KaiC-like domain / KaiC / CheY-like superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Circadian clock oscillator protein KaiC / Circadian clock oscillator protein KaiB / Circadian clock oscillator protein KaiA
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsTseng, R. / Goularte, N.F. / Chavan, A. / Luu, J. / Chang, Y.G. / Heilser, J. / Tripathi, S. / LiWang, A. / Partch, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107521 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107069 United States
CitationJournal: Science / Year: 2017
Title: Structural basis of the day-night transition in a bacterial circadian clock.
Authors: Tseng, R. / Goularte, N.F. / Chavan, A. / Luu, J. / Cohen, S.E. / Chang, Y.G. / Heisler, J. / Li, S. / Michael, A.K. / Tripathi, S. / Golden, S.S. / LiWang, A. / Partch, C.L.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 kinase KaiC
B: Circadian clock protein KaiB
C: Circadian clock protein kinase KaiC
D: Circadian clock protein KaiB
E: Circadian clock protein KaiA
F: Circadian clock protein KaiA
G: Circadian clock protein KaiA
H: Circadian clock protein KaiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,87910
Polymers146,6898
Non-polymers1902
Water1,910106
1
A: Circadian clock protein kinase KaiC
B: Circadian clock protein KaiB
E: Circadian clock protein KaiA
F: Circadian clock protein KaiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4405
Polymers73,3454
Non-polymers951
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-38 kcal/mol
Surface area27230 Å2
MethodPISA
2
C: Circadian clock protein kinase KaiC
D: Circadian clock protein KaiB
G: Circadian clock protein KaiA
H: Circadian clock protein KaiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4405
Polymers73,3454
Non-polymers951
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-33 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.595, 79.105, 80.838
Angle α, β, γ (deg.)107.27, 90.71, 111.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Circadian clock protein kinase KaiC


Mass: 27738.166 Da / Num. of mol.: 2 / Mutation: R41A, K173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: kaiC, tlr0483 / Plasmid: pET-28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q79V60, non-specific serine/threonine protein kinase
#2: Protein Circadian clock protein KaiB


Mass: 10941.011 Da / Num. of mol.: 2 / Mutation: Y8A, G89A, D91R, Y94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: kaiB, tlr0482 / Plasmid: pET-28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q79V61
#3: Protein
Circadian clock protein KaiA


Mass: 17332.758 Da / Num. of mol.: 4 / Mutation: C272S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: kaiA, tlr0481 / Plasmid: pET-28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q79V62
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.15M Ammonium Sulfate, 0.1M Tris pH 7.0, 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 47380 / % possible obs: 96.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.53 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→44.841 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.09
RfactorNum. reflection% reflection
Rfree0.242 2324 4.91 %
Rwork0.1847 --
obs0.1876 47363 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.61→44.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9412 0 10 106 9528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049578
X-RAY DIFFRACTIONf_angle_d0.92312915
X-RAY DIFFRACTIONf_dihedral_angle_d14.5253648
X-RAY DIFFRACTIONf_chiral_restr0.0371483
X-RAY DIFFRACTIONf_plane_restr0.0041643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6095-2.66280.3521110.28472276X-RAY DIFFRACTION81
2.6628-2.72070.30671310.26932720X-RAY DIFFRACTION97
2.7207-2.7840.35781380.26092700X-RAY DIFFRACTION98
2.784-2.85360.32171510.25272667X-RAY DIFFRACTION97
2.8536-2.93070.31081280.24792711X-RAY DIFFRACTION98
2.9307-3.01690.31221280.23232717X-RAY DIFFRACTION98
3.0169-3.11430.31891650.22832711X-RAY DIFFRACTION97
3.1143-3.22560.27811490.22372688X-RAY DIFFRACTION97
3.2256-3.35470.26631600.20672666X-RAY DIFFRACTION97
3.3547-3.50730.2451320.20062680X-RAY DIFFRACTION97
3.5073-3.69210.23991340.17782661X-RAY DIFFRACTION96
3.6921-3.92330.22891350.1772654X-RAY DIFFRACTION95
3.9233-4.2260.19651190.16142644X-RAY DIFFRACTION96
4.226-4.65090.18211440.1392656X-RAY DIFFRACTION95
4.6509-5.3230.22211530.15142654X-RAY DIFFRACTION96
5.323-6.70280.2511090.18022723X-RAY DIFFRACTION97
6.7028-44.84760.19921370.14442511X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.18130.39090.89152.39610.58892.19480.07320.0990.01810.42480.2022-0.31080.17850.03090.15710.32590.0551-0.06820.2383-0.0270.275138.486843.529152.7018
20.5049-0.0341-0.05140.5895-0.03330.6036-0.0501-0.2796-0.17980.12890.0915-0.03780.0006-0.43850.03360.247-0.01870.04930.46870.04720.2610.222240.389336.1514
31.70780.34430.34292.15960.8181.7654-0.2812-0.1233-0.1319-0.7304-0.11930.5381-0.2736-0.0531-0.34410.4780.0251-0.24320.2156-0.06010.374438.316712.542336.0725
40.8808-0.00540.5110.48090.13970.4220.1722-0.1324-0.11280.1238-0.03140.14630.1354-0.30750.02110.2038-0.0440.0780.29120.02550.262248.01759.736767.3263
51.13540.4814-0.34470.9542-0.17892.1047-0.0343-0.0421-0.07040.07160.0919-0.0564-0.5409-0.20250.04950.3140.07810.02750.2602-0.0030.17815.037558.199520.3854
61.0410.19480.08330.9628-0.02271.508-0.19180.2805-0.0232-0.32460.0942-0.0064-0.1003-0.0143-0.01790.3009-0.0440.05710.28930.00770.185423.267449.67065.5114
71.43771.1080.15860.820.67111.86370.14780.0743-0.49540.12250.1126-0.2407-0.0284-0.2520.17070.1682-0.0389-0.01140.1720.03220.428470.05011.849861.3888
80.78641.04970.22151.24850.27881.1696-0.02310.0262-0.17680.2487-0.0039-0.4324-0.41390.2581-0.01830.223-0.04670.040.33370.01820.337880.363217.508659.9536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 18 through 250)
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 94)
3X-RAY DIFFRACTION3(chain 'C' and resid 18 through 249)
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 92)
5X-RAY DIFFRACTION5(chain 'E' and resid 150 through 281)
6X-RAY DIFFRACTION6(chain 'F' and resid 149 through 282)
7X-RAY DIFFRACTION7(chain 'G' and resid 149 through 281)
8X-RAY DIFFRACTION8(chain 'H' and resid 148 through 282)

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