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- PDB-5f68: Drosophila Melanogaster Cycle W398A PAS-B with Bound Ethylene Glycol -

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Basic information

Entry
Database: PDB / ID: 5f68
TitleDrosophila Melanogaster Cycle W398A PAS-B with Bound Ethylene Glycol
ComponentsProtein cycle
KeywordsCIRCADIAN CLOCK PROTEIN / PAS / Ethylene Glycol / Clock / BMAL
Function / homology
Function and homology information


Transcription regulation of cwo gene / Transcription activation by CLK:CYC and repression by VRI / NPAS4 regulates expression of target genes / circadian regulation of heart rate / Circadian Clock pathway / eclosion rhythm / Transcription repression by PER and activation by PDP1 / Dephosphorylation of PER / Degradation of PER / Degradation of TIM ...Transcription regulation of cwo gene / Transcription activation by CLK:CYC and repression by VRI / NPAS4 regulates expression of target genes / circadian regulation of heart rate / Circadian Clock pathway / eclosion rhythm / Transcription repression by PER and activation by PDP1 / Dephosphorylation of PER / Degradation of PER / Degradation of TIM / rhythmic behavior / regulation of circadian sleep/wake cycle, sleep / aryl hydrocarbon receptor complex / response to starvation / locomotor rhythm / behavioral response to cocaine / circadian regulation of gene expression / circadian rhythm / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / Nuclear translocator / Helix-loop-helix DNA-binding domain / PAS domain / PAS domain / Beta-Lactamase / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily ...: / Nuclear translocator / Helix-loop-helix DNA-binding domain / PAS domain / PAS domain / Beta-Lactamase / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.23 Å
AuthorsManahan, C.C. / Crane, B.R.
CitationJournal: To Be Published
Title: Drosophila Melanogaster Cycle PAS-B with Bound Ethylene Glycol
Authors: Manahan, C.C. / Crane, B.R.
History
DepositionDec 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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: Protein cycle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1692
Polymers12,1071
Non-polymers621
Water1,928107
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint3 kcal/mol
Surface area6000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.308, 44.169, 38.574
Angle α, β, γ (deg.)90.000, 115.160, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein cycle / Brain and muscle ARNT-like 1 / BMAL1 / MOP3


Mass: 12106.827 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cyc, CG8727 / Production host: Escherichia coli (E. coli) / References: UniProt: O61734
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. obs: 30239 / % possible obs: 93.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.066 / Rrim(I) all: 0.121 / Χ2: 3.029 / Net I/av σ(I): 12.084 / Net I/σ(I): 5 / Num. measured all: 95323
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.23-1.2520.54110320.5660.430.6950.48363.9
1.25-1.272.30.54711760.6950.4080.6860.48372.6
1.27-1.32.60.56112440.6590.3940.6890.45976.7
1.3-1.322.70.5712980.6740.3950.6970.47381.5
1.32-1.352.80.52613970.6980.3580.6390.45786.9
1.35-1.3930.50114890.7470.3390.6080.4591.7
1.39-1.423.10.46515250.7280.3160.5640.47295.6
1.42-1.4630.41415850.790.2780.5010.50998.2
1.46-1.53.20.35515970.8820.2340.4270.50799.3
1.5-1.553.50.31816150.8960.20.3760.51100
1.55-1.613.50.25516300.9370.160.3020.521100
1.61-1.673.50.21216000.9530.1330.2510.541100
1.67-1.753.30.16516140.970.1060.1970.60899.8
1.75-1.843.20.12816420.9760.0840.1540.657100
1.84-1.953.60.10815970.9840.0670.1270.796100
1.95-2.13.50.08616290.9880.0540.1010.925100
2.1-2.313.30.0716100.990.0450.0831.00399.9
2.31-2.653.50.06216320.9930.0390.0741.06100
2.65-3.343.40.0516520.9950.0320.061.22999.9
3.34-503.40.08416750.9690.0530.139.483100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementResolution: 1.23→34.915 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 1994 6.61 %
Rwork0.1799 28178 -
obs0.181 30172 92.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.69 Å2 / Biso mean: 14.5717 Å2 / Biso min: 5.47 Å2
Refinement stepCycle: final / Resolution: 1.23→34.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms852 0 4 107 963
Biso mean--15.81 25.86 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012883
X-RAY DIFFRACTIONf_angle_d1.2661189
X-RAY DIFFRACTIONf_chiral_restr0.123126
X-RAY DIFFRACTIONf_plane_restr0.01152
X-RAY DIFFRACTIONf_dihedral_angle_d13.837325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2304-1.26110.2464980.25091393149164
1.2611-1.29520.26751140.25351599171374
1.2952-1.33340.26691240.24261775189982
1.3334-1.37640.29421370.24371914205189
1.3764-1.42560.22281450.22742048219395
1.4256-1.48270.2111510.21152137228898
1.4827-1.55010.20221500.194821282278100
1.5501-1.63190.19481540.172821712325100
1.6319-1.73410.17611520.157721432295100
1.7341-1.8680.17391530.166221642317100
1.868-2.0560.1761530.156121632316100
2.056-2.35340.1941550.158221842339100
2.3534-2.96480.18871540.181221802334100
2.9648-34.92950.18361540.16942179233398
Refinement TLS params.Method: refined / Origin x: 80.4771 Å / Origin y: 17.9789 Å / Origin z: 16.7144 Å
111213212223313233
T0.0658 Å2-0.0015 Å20.0036 Å2-0.0595 Å2-0.0029 Å2--0.0646 Å2
L0.3955 °20.2587 °20.0807 °2-0.4453 °2-0.086 °2--0.2463 °2
S0.0111 Å °0.0064 Å °-0.0081 Å °-0.017 Å °0.0166 Å °-0.0177 Å °-0.0162 Å °-0.0004 Å °0.0122 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA310 - 412
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 111

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