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- PDB-1r5q: Crystal Structure Analysis of Kai A from PCC7120 -

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Basic information

Entry
Database: PDB / ID: 1r5q
TitleCrystal Structure Analysis of Kai A from PCC7120
Componentscircadian oscillation regulator
KeywordsGENE REGULATION / FOUR-HELIX-BUNDLE
Function / homology
Function and homology information


circadian rhythm / protein phosphorylation
Similarity search - Function
KaiA/RbsU domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Circadian clock protein KaiA
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 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: Derived calculations / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: circadian oscillation regulator


Theoretical massNumber of molelcules
Total (without water)11,9791
Polymers11,9791
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: circadian oscillation regulator

A: circadian oscillation regulator


Theoretical massNumber of molelcules
Total (without water)23,9582
Polymers23,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area1880 Å2
ΔGint-19 kcal/mol
Surface area10680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.299, 57.299, 137.515
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein circadian oscillation regulator / Kai A


Mass: 11978.903 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: Kai A / Plasmid: pET32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl 21 / References: UniProt: Q8YT42
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MgSO4, pH 6.0, 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-B20.940707, 0.9188, 0.9192259
Detector
TypeIDDetectorDate
MARRESEARCH1CCDNov 16, 2002
MARRESEARCH2CCDNov 16, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9407071
30.91881
40.91922591
ReflectionResolution: 2→60 Å / Num. obs: 9566 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 29.8 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→24.42 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 665115.44 / 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
Rfree0.269 865 10.6 %RANDOM
Rwork0.241 ---
obs-8144 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.8921 Å2 / ksol: 0.429491 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å23.23 Å20 Å2
2---1.25 Å20 Å2
3---2.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→24.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 0 38 790
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shellResolution: 2→2.23 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 137 10.4 %
Rwork0.245 1175 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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