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- PDB-5svv: Structure and kinetics of the LOV domain of ZEITLUPE determine it... -

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Basic information

Entry
Database: PDB / ID: 5svv
TitleStructure and kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis
ComponentsAdagio protein 1
KeywordsCIRCADIAN CLOCK PROTEIN / LOV / Kinetics / PAS domain / photoreceptor
Function / homology
Function and homology information


flower development / photoreceptor activity / rhythmic process / protein ubiquitination / nucleus / cytoplasm
Similarity search - Function
Kelch repeat type 2 / Kelch motif / A Receptor for Ubiquitination Targets / F-box domain profile. / Galactose oxidase/kelch, beta-propeller / F-box-like / F-box-like domain superfamily / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / F-box domain / PAS domain ...Kelch repeat type 2 / Kelch motif / A Receptor for Ubiquitination Targets / F-box domain profile. / Galactose oxidase/kelch, beta-propeller / F-box-like / F-box-like domain superfamily / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / F-box domain / PAS domain / Kelch-type beta propeller / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / Adagio protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsZoltowski, B. / Pudasaini, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15GM109282 United States
CitationJournal: Elife / Year: 2017
Title: Kinetics of the LOV domain of ZEITLUPE determine its circadian function inArabidopsis.
Authors: Pudasaini, A. / Shim, J.S. / Song, Y.H. / Shi, H. / Kiba, T. / Somers, D.E. / Imaizumi, T. / Zoltowski, B.D.
History
DepositionAug 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 28, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.4Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 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
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
D: Adagio protein 1
A: Adagio protein 1
B: Adagio protein 1
C: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,82113
Polymers61,6354
Non-polymers2,1879
Water6,179343
1
D: Adagio protein 1
C: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8816
Polymers30,8172
Non-polymers1,0644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-21 kcal/mol
Surface area12740 Å2
MethodPISA
2
A: Adagio protein 1
B: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9407
Polymers30,8172
Non-polymers1,1235
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-28 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.427, 85.427, 198.775
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Adagio protein 1 / Clock-associated PAS protein ZTL / F-box only protein 2b / FBX2b / Flavin-binding kelch repeat F- ...Clock-associated PAS protein ZTL / F-box only protein 2b / FBX2b / Flavin-binding kelch repeat F-box protein 1-like protein 2 / FKF1-like protein 2 / LOV kelch protein 1 / Protein ZEITLUPE


Mass: 15408.677 Da / Num. of mol.: 4 / Fragment: LOV domain (UNP residues 29-165) / Mutation: V48I, G80R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADO1, FKL2, LKP1, ZTL, At5g57360, MSF19.2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q94BT6
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Mutation: V48I, G80R
Source method: isolated from a genetically manipulated source
Formula: C17H21N4O9P
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 3.41 Å3/Da / Density % sol: 63.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris ph 8.5, 0.2 M Sodium Acetate trihydrate, 30% w/v PEG 4K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 49510 / % possible obs: 99.3 % / Redundancy: 7.9 % / Net I/σ(I): 36.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 12.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D72

3d72


Resolution: 2.101→36.367 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2002 2511 5.07 %
Rwork0.163 --
obs0.1649 49486 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.101→36.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 148 343 4427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124227
X-RAY DIFFRACTIONf_angle_d1.4645749
X-RAY DIFFRACTIONf_dihedral_angle_d19.0181584
X-RAY DIFFRACTIONf_chiral_restr0.067628
X-RAY DIFFRACTIONf_plane_restr0.007742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1008-2.14120.22911220.1982554X-RAY DIFFRACTION98
2.1412-2.18490.22331520.18312583X-RAY DIFFRACTION100
2.1849-2.23240.22161400.1782590X-RAY DIFFRACTION100
2.2324-2.28440.21971280.17032589X-RAY DIFFRACTION100
2.2844-2.34150.18171510.16652553X-RAY DIFFRACTION100
2.3415-2.40480.20841470.16212626X-RAY DIFFRACTION100
2.4048-2.47550.19181460.16212570X-RAY DIFFRACTION100
2.4755-2.55540.2031450.1642599X-RAY DIFFRACTION100
2.5554-2.64670.21651380.16372618X-RAY DIFFRACTION100
2.6467-2.75270.19981380.16672628X-RAY DIFFRACTION100
2.7527-2.87790.2371050.17132629X-RAY DIFFRACTION100
2.8779-3.02950.20011420.16522637X-RAY DIFFRACTION100
3.0295-3.21920.23431480.16442609X-RAY DIFFRACTION100
3.2192-3.46760.21151400.16132634X-RAY DIFFRACTION100
3.4676-3.81630.17661660.14752633X-RAY DIFFRACTION100
3.8163-4.36770.16611440.14752644X-RAY DIFFRACTION99
4.3677-5.49980.18121390.14472635X-RAY DIFFRACTION97
5.4998-36.37210.2261200.19412644X-RAY DIFFRACTION92

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