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- PDB-2qke: Wild Type Crystal Structure of Full Length Circadian Clock Protei... -

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Basic information

Entry
Database: PDB / ID: 2qke
TitleWild Type Crystal Structure of Full Length Circadian Clock Protein KaiB from Thermosynechococcus elongatus BP-1
ComponentsCircadian clock protein kaiB
KeywordsCIRCADIAN CLOCK PROTEIN / CYANOBACTERIAL CIRCADIAN CLOCK PROTEIN
Function / homology
Function and homology information


negative regulation of phosphorylation / circadian rhythm
Similarity search - Function
Circadian clock protein KaiB / Circadian clock protein KaiB-like / KaiB domain / KaiB domain / KaiB / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Circadian clock oscillator protein KaiB
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPattanayek, R. / Egli, M. / Pattanayek, S.
CitationJournal: Embo J. / Year: 2008
Title: Structural model of the circadian clock KaiB-KaiC complex and mechanism for modulation of KaiC phosphorylation.
Authors: Pattanayek, R. / Williams, D.R. / Pattanayek, S. / Mori, T. / Johnson, C.H. / Stewart, P.L. / Egli, M.
History
DepositionJul 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 kaiB
B: Circadian clock protein kaiB
C: Circadian clock protein kaiB
D: Circadian clock protein kaiB
E: Circadian clock protein kaiB
F: Circadian clock protein kaiB


Theoretical massNumber of molelcules
Total (without water)72,2406
Polymers72,2406
Non-polymers00
Water1,13563
1
A: Circadian clock protein kaiB
B: Circadian clock protein kaiB

E: Circadian clock protein kaiB
F: Circadian clock protein kaiB


Theoretical massNumber of molelcules
Total (without water)48,1604
Polymers48,1604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area6440 Å2
ΔGint-44.3 kcal/mol
Surface area21330 Å2
MethodPISA
2
C: Circadian clock protein kaiB
D: Circadian clock protein kaiB

C: Circadian clock protein kaiB
D: Circadian clock protein kaiB


Theoretical massNumber of molelcules
Total (without water)48,1604
Polymers48,1604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7110 Å2
ΔGint-36.8 kcal/mol
Surface area19580 Å2
MethodPISA
3
A: Circadian clock protein kaiB
B: Circadian clock protein kaiB


Theoretical massNumber of molelcules
Total (without water)24,0802
Polymers24,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-10.8 kcal/mol
Surface area12620 Å2
MethodPISA
4
C: Circadian clock protein kaiB
D: Circadian clock protein kaiB


Theoretical massNumber of molelcules
Total (without water)24,0802
Polymers24,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-9.4 kcal/mol
Surface area11770 Å2
MethodPISA
5
E: Circadian clock protein kaiB
F: Circadian clock protein kaiB


Theoretical massNumber of molelcules
Total (without water)24,0802
Polymers24,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-10.3 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.132, 191.218, 34.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Circadian clock protein kaiB /


Mass: 12040.047 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Species: Thermosynechococcus elongatus / Strain: BP-1 / References: UniProt: Q79V61
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10% PEG 3350, 10% DMSO, 0.1M ACETATE BUFFER, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9798 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18443 / % possible obs: 87 % / Observed criterion σ(I): 3.4 / Redundancy: 7 % / Biso Wilson estimate: 82.9 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 3.4
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 7.1 / % possible all: 60.4

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VGL

1vgl


Resolution: 2.7→44.4 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.284 1520 random
Rwork0.233 --
obs0.233 13727 -
Displacement parametersBiso mean: 82.9 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 0 63 4871
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 2.7→2.73 Å /
RfactorNum. reflection
Rfree0.798 22
Rwork0.564 -

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