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- PDB-1r5p: Crystal Structure Analysis of KaiB from PCC7120 -

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Basic information

Entry
Database: PDB / ID: 1r5p
TitleCrystal Structure Analysis of KaiB from PCC7120
Componentscircadian oscillation regulator
KeywordsGENE REGULATION / ALPHA-BETA MEANDER / PROTEIN DIMER
Function / homology
Function and homology information


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 speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsGarces, R.G. / Wu, N. / Gillon, W. / Pai, E.F.
CitationJournal: Embo J. / Year: 2004
Title: Anabaena circadian clock proteins KaiA and KaiB reveal a potential common binding site to their partner KaiC
Authors: Garces, R.G. / Wu, N. / Gillon, W. / Pai, E.F.
History
DepositionOct 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: circadian oscillation regulator
B: circadian oscillation regulator


Theoretical massNumber of molelcules
Total (without water)24,5822
Polymers24,5822
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-9 kcal/mol
Surface area9870 Å2
MethodPISA
2
A: circadian oscillation regulator
B: circadian oscillation regulator

A: circadian oscillation regulator
B: circadian oscillation regulator


Theoretical massNumber of molelcules
Total (without water)49,1654
Polymers49,1654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6520 Å2
ΔGint-41 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.755, 36.387, 54.140
Angle α, β, γ (deg.)90.00, 98.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-123-

HOH

21A-135-

HOH

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Components

#1: Protein circadian oscillation regulator / KaiB


Mass: 12291.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: KaiB / Plasmid: pET32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8YT41
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
22001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-ID-B11
SYNCHROTRONAPS 14-ID-B20.95705, 0.97943, 0.97971
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 21, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.957051
30.979431
40.979711
ReflectionResolution: 2.2→60 Å / Num. obs: 10484 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 15.9 Å2
Reflection shellResolution: 2.2→2.44 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→25.88 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 554402.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 602 5.9 %RANDOM
Rwork0.212 ---
obs-10159 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.8366 Å2 / ksol: 0.415646 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1--6.26 Å20 Å21.08 Å2
2--19.25 Å20 Å2
3----12.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→25.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 0 67 1519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 138 8.4 %
Rwork0.229 1506 -
obs--95.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM

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