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- PDB-3gec: Crystal structure of a tandem PAS domain fragment of Drosophila PERIOD -

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Basic information

Entry
Database: PDB / ID: 3gec
TitleCrystal structure of a tandem PAS domain fragment of Drosophila PERIOD
ComponentsPeriod circadian protein
KeywordsCIRCADIAN CLOCK PROTEIN / monomeric PAS repeat fragment / Alternative splicing / Biological rhythms / Cytoplasm / Nucleus / Phosphoprotein / Polymorphism
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 / mating behavior / circadian 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 / regulation of protein phosphorylation / circadian regulation of gene expression / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Period circadian protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsYildiz, O. / Wolf, E.
CitationJournal: Plos Biol. / Year: 2009
Title: Structural and functional analyses of PAS domain interactions of the clock proteins Drosophila PERIOD and mouse PERIOD2
Authors: Hennig, S. / Strauss, H.M. / Vanselow, K. / Yildiz, O. / Schulze, S. / Arens, J. / Kramer, A. / Wolf, E.
History
DepositionFeb 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Period circadian protein


Theoretical massNumber of molelcules
Total (without water)34,9401
Polymers34,9401
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.950, 114.950, 85.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 34940.168 Da / Num. of mol.: 1 / Fragment: PAS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: per / Plasmid: pGEX6P2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07663

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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: 4.68 Å3/Da / Density % sol: 73.71 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 70mM Sodiumtartrate, 20mM Hepes, 5mM DTE, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4→19.68 Å / Num. obs: 5578 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 136.8 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.061 / Net I/σ(I): 18.07
Reflection shellResolution: 4→4.1 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3.82 / Num. unique all: 408 / Rsym value: 0.469 / % possible all: 97.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WA9

1wa9


Resolution: 4→19.68 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.312 279 -RANDOM
Rwork0.244 ---
all0.247 5710 --
obs0.247 5576 97.7 %-
Displacement parametersBiso mean: 151.3 Å2
Baniso -1Baniso -2Baniso -3
1-22.01 Å20 Å20 Å2
2--22.01 Å20 Å2
3----44.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a1.44 Å0.81 Å
Refinement stepCycle: LAST / Resolution: 4→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 0 0 2054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_torsion_deg25.5
X-RAY DIFFRACTIONc_torsion_impr_deg1.09
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
4-4.180.448340.2980.07768498.7
4.18-4.40.27350.2170.04670898.9
4.4-4.670.211340.1690.03667698.8
4.67-5.030.239360.1960.0471097.9
5.03-5.520.359350.2190.06170198.6
5.52-6.30.335340.2320.05768097.6

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