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- PDB-1r8j: Crystal Structure of Circadian Clock Protein KaiA from Synechococ... -

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Basic information

Entry
Database: PDB / ID: 1r8j
TitleCrystal Structure of Circadian Clock Protein KaiA from Synechococcus elongatus
ComponentsKaiA
KeywordsCIRCADIAN CLOCK PROTEIN / KaiA
Function / homology
Function and homology information


detection of redox state / : / entrainment of circadian clock / positive regulation of circadian rhythm / circadian rhythm / 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 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / CheY-like superfamily / Response regulator / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Circadian clock oscillator protein KaiA
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / combination of SAD phasing, real space molecular replacement, ARP/wARP phase improvement, and non-crystallographic symmetry averaging / Resolution: 2.03 Å
AuthorsYe, S. / Vakonakis, I. / Sacchettini, J.C. / LiWang, A.C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of circadian clock protein KaiA from Synechococcus elongatus
Authors: Ye, S. / Vakonakis, I. / Ioerger, T.R. / LiWang, A.C. / Sacchettini, J.C.
History
DepositionOct 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KaiA
B: KaiA


Theoretical massNumber of molelcules
Total (without water)66,2712
Polymers66,2712
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-26 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.111, 125.818, 56.818
Angle α, β, γ (deg.)90.00, 114.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein KaiA


Mass: 33135.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria)
Species: Synechococcus elongatus / Strain: Pcc 7942 / Gene: KaiA / Plasmid: pET32a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q79PF6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: Ammonium Sulfate, Sodium Cacodylate, PEG 8000, Glycerol, pH 6.5, EVAPORATION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 38494 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 30.6
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.362 / % possible all: 54.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: combination of SAD phasing, real space molecular replacement, ARP/wARP phase improvement, and non-crystallographic symmetry averaging
Starting model: PDB ENTRY 1M2E

1m2e


Resolution: 2.03→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.615 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27144 1905 5 %RANDOM
Rwork0.21012 ---
obs0.21306 36552 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å21.54 Å2
2---0.36 Å20 Å2
3---2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.03→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4331 0 0 246 4577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214408
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9615967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3895530
X-RAY DIFFRACTIONr_chiral_restr0.0830.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023334
X-RAY DIFFRACTIONr_nbd_refined0.1920.21964
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.212
X-RAY DIFFRACTIONr_mcbond_it0.7561.52682
X-RAY DIFFRACTIONr_mcangle_it1.43624333
X-RAY DIFFRACTIONr_scbond_it1.74531726
X-RAY DIFFRACTIONr_scangle_it2.9284.51634
LS refinement shellResolution: 2.03→2.078 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 101
Rwork0.255 2393

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