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- PDB-3rty: Structure of an Enclosed Dimer Formed by The Drosophila Period Protein -

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Basic information

Entry
Database: PDB / ID: 3rty
TitleStructure of an Enclosed Dimer Formed by The Drosophila Period Protein
ComponentsPeriod circadian protein
KeywordsCIRCADIAN CLOCK PROTEIN / PAS domain / signalling / Timeless
Function / homology
Function and homology information


Nuclear import of PER and TIM / Dephosphorylation of TIM / eclosion rhythm / Transcription repression by PER and activation by PDP1 / Dephosphorylation of PER / Phosphorylation of PER and TIM / copulation / Degradation of PER / Degradation of TIM / courtship behavior ...Nuclear import of PER and TIM / Dephosphorylation of TIM / eclosion rhythm / Transcription repression by PER and activation by PDP1 / Dephosphorylation of PER / Phosphorylation of PER and TIM / copulation / Degradation of PER / Degradation of TIM / courtship behavior / male courtship behavior, veined wing generated song production / circadian temperature homeostasis / rhythmic behavior / circadian sleep/wake cycle / regulation of locomotor rhythm / regulation of circadian sleep/wake cycle, sleep / entrainment of circadian clock / circadian behavior / mating behavior / response to temperature stimulus / entrainment of circadian clock by photoperiod / locomotor rhythm / behavioral response to cocaine / response to light stimulus / long-term memory / transcription corepressor binding / determination of adult lifespan / transcription coregulator activity / circadian regulation of gene expression / regulation of protein phosphorylation / regulation of circadian rhythm / circadian rhythm / transcription corepressor activity / cell body / response to oxidative stress / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / PAS domain / PAS domain / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily ...: / PAS domain / PAS domain / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Period circadian protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsKing, H.A. / Hoelz, A. / Crane, B.R. / Young, M.W.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure of an enclosed dimer formed by the Drosophila period protein.
Authors: King, H.A. / Hoelz, A. / Crane, B.R. / Young, M.W.
History
DepositionMay 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Period circadian protein
B: Period circadian protein
C: Period circadian protein
D: Period circadian protein
E: Period circadian protein
F: Period circadian protein
G: Period circadian protein
H: Period circadian protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,81436
Polymers305,4958
Non-polymers4,31928
Water4,197233
1
A: Period circadian protein
B: Period circadian protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,60810
Polymers76,3742
Non-polymers1,2348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-76 kcal/mol
Surface area30910 Å2
MethodPISA
2
C: Period circadian protein
D: Period circadian protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4549
Polymers76,3742
Non-polymers1,0807
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-73 kcal/mol
Surface area30780 Å2
MethodPISA
3
E: Period circadian protein
F: Period circadian protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2998
Polymers76,3742
Non-polymers9266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-74 kcal/mol
Surface area30880 Å2
MethodPISA
4
G: Period circadian protein
H: Period circadian protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4549
Polymers76,3742
Non-polymers1,0807
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-75 kcal/mol
Surface area30760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.414, 94.697, 141.030
Angle α, β, γ (deg.)88.19, 89.63, 89.87
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Period circadian protein / Protein clock-6 / CLK-6


Mass: 38186.922 Da / Num. of mol.: 8 / Fragment: central fragment (UNP residues 236-574)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: per, CG2647 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07663
#2: Chemical...
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 200 mM lithium chloride, 20 % (w/v) PEG 3350, 100 mM Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 62952 / % possible obs: 92.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 87.3 Å2 / Rsym value: 0.081 / Net I/σ(I): 14.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→20.01 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 74354.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.289 6399 10.2 %RANDOM
Rwork0.239 ---
obs0.239 62959 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.1009 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 70.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.58 Å22.55 Å21.42 Å2
2--3.28 Å2-1.29 Å2
3----8.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.85→20.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19391 0 224 233 19848
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.41
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it3.082
X-RAY DIFFRACTIONc_scbond_it6.272
X-RAY DIFFRACTIONc_scangle_it7.632.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 889 10.7 %
Rwork0.345 7443 -
obs--68.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6DTT.top

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