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- PDB-1wa9: Crystal Structure of the PAS repeat region of the Drosophila cloc... -

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Basic information

Entry
Database: PDB / ID: 1wa9
TitleCrystal Structure of the PAS repeat region of the Drosophila clock protein PERIOD
ComponentsPERIOD CIRCADIAN PROTEIN
KeywordsCIRCADIAN RHYTHM / PERIOD / PAS DOMAIN / CLOCK PROTEIN / PHOSPHORYLATION / 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
Single helix bin / PAS domain / PAS domain / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily ...Single helix bin / PAS domain / PAS domain / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Period circadian protein
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.15 Å
AuthorsYildiz, O. / Doi, M. / Yujnovsky, I. / Cardone, L. / Berndt, A. / Hennig, S. / Schulze, S. / Urbanke, C. / Sassone-Corsi, P. / Wolf, E.
CitationJournal: Mol.Cell / Year: 2005
Title: Crystal Structure and Interactions of the Pas Repeat Region of the Drosophila Clock Protein Period
Authors: Yildiz, O. / Doi, M. / Yujnovsky, I. / Cardone, L. / Berndt, A. / Hennig, S. / Schulze, S. / Urbanke, C. / Sassone-Corsi, P. / Wolf, E.
History
DepositionOct 25, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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


Theoretical massNumber of molelcules
Total (without water)82,9152
Polymers82,9152
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)140.440, 140.440, 61.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9529, 0.0677, -0.2955), (0.0353, -0.9433, -0.33), (-0.3011, -0.3248, 0.8966)
Vector: 226.9669, 133.1289, 57.6181)

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Components

#1: Protein PERIOD CIRCADIAN PROTEIN / CLOCK-6 PROTEIN / CLK-6


Mass: 41457.469 Da / Num. of mol.: 2 / Fragment: PAS REPEAT REGION, RESIDUES 232-599
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07663
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.7 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.7 / Details: 500 MM CALCIUM CHLORIDE, pH 7.70

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 19, 2002 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.15→25 Å / Num. obs: 21048 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 87.6 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.06 / Net I/σ(I): 18.1
Reflection shellResolution: 3.15→3.25 Å / Redundancy: 5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.38 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 3.15→25 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 1053 5 %RANDOM
Rwork0.2279 ---
obs0.2279 21045 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.4308 Å2 / ksol: 0.213266 e/Å3
Displacement parametersBiso mean: 63.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.702 Å20 Å20 Å2
2--1.702 Å20 Å2
3----3.403 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 3.15→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5033 0 0 6 5039
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009296
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_deg1.51092
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.15→3.26 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.516 104 5 %
Rwork0.42 1978 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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