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- PDB-1wwj: crystal structure of KaiB from Synechocystis sp. -

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Basic information

Entry
Database: PDB / ID: 1wwj
Titlecrystal structure of KaiB from Synechocystis sp.
ComponentsCircadian clock protein kaiB
KeywordsCIRCADIAN CLOCK PROTEIN / circadian / clock
Function / homology
Function and homology information


negative regulation of phosphorylation / circadian rhythm / identical protein binding
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
TRIMETHYL GLYCINE / IMIDAZOLE / D-MALATE / Circadian clock protein KaiB
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHitomi, K. / Oyama, T. / Han, S. / Arvai, A.S. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Tetrameric architecture of the circadian clock protein KaiB. A novel interface for intermolecular interactions and its impact on the circadian rhythm.
Authors: Hitomi, K. / Oyama, T. / Han, S. / Arvai, A.S. / Getzoff, E.D.
History
DepositionJan 6, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 kaiB
B: Circadian clock protein kaiB
C: Circadian clock protein kaiB
D: Circadian clock protein kaiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,67520
Polymers47,8044
Non-polymers1,87116
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-34 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.770, 66.036, 114.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Circadian clock protein kaiB /


Mass: 11950.994 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P74645
#2: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical
ChemComp-BET / TRIMETHYL GLYCINE / Trimethylglycine


Mass: 118.154 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H12NO2
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 41.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: betaine, pH 6.0, VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 31143 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.2 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 89.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.04 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1050233.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1450 4.9 %RANDOM
Rwork0.25 ---
obs0.25 29369 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 88.641 Å2 / ksol: 0.375667 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1--9.39 Å20 Å20 Å2
2--19.13 Å20 Å2
3----9.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 127 237 3431
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.742
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 181 4.7 %
Rwork0.298 3636 -
obs--71.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4IMD_MLT.PARIMD_MLT.TOP
X-RAY DIFFRACTION5BET_XPLOR_PAR.TXTBET_XPLOR_TOP.TXT

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