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

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Basic information

Entry
Database: PDB / ID: 5svu
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


response to blue light / flower development / SCF ubiquitin ligase complex / photoreceptor activity / circadian rhythm / protein ubiquitination / nucleus / cytosol
Similarity search - Function
Kelch repeat type 2 / Kelch motif / Galactose oxidase, central domain / Galactose oxidase, central domain / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / Galactose oxidase/kelch, beta-propeller / F-box-like / F-box domain ...Kelch repeat type 2 / Kelch motif / Galactose oxidase, central domain / Galactose oxidase, central domain / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / Galactose oxidase/kelch, beta-propeller / F-box-like / 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
FLAVIN MONONUCLEOTIDE / Adagio protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 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
B: Adagio protein 1
A: Adagio protein 1
C: Adagio protein 1
D: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4048
Polymers61,5794
Non-polymers1,8254
Water2,504139
1
B: Adagio protein 1
A: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7024
Polymers30,7892
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-27 kcal/mol
Surface area13080 Å2
MethodPISA
2
C: Adagio protein 1
D: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7024
Polymers30,7892
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-20 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.351, 85.351, 200.000
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: 15394.649 Da / Num. of mol.: 4 / Fragment: LOV domain (UNP residues 29-165) / Mutation: 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 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.5, 0.2 M Magnesium Chloride hexahydrate, 30% w/v PEG 4k

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9173 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26153 / % possible obs: 97.9 % / Redundancy: 10 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 55.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 7.8 / % possible all: 86.8

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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: 2.601→49.506 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1312 5.02 %
Rwork0.1642 --
obs0.1676 26136 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.601→49.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 124 139 4241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144208
X-RAY DIFFRACTIONf_angle_d1.6085724
X-RAY DIFFRACTIONf_dihedral_angle_d19.8571573
X-RAY DIFFRACTIONf_chiral_restr0.065630
X-RAY DIFFRACTIONf_plane_restr0.007735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6011-2.70520.29971390.21012745X-RAY DIFFRACTION100
2.7052-2.82830.25631440.20642782X-RAY DIFFRACTION100
2.8283-2.97740.26151440.20622772X-RAY DIFFRACTION100
2.9774-3.1640.30361590.19232787X-RAY DIFFRACTION100
3.164-3.40820.26911460.1862798X-RAY DIFFRACTION100
3.4082-3.75110.2371660.16082747X-RAY DIFFRACTION99
3.7511-4.29360.2031290.14072776X-RAY DIFFRACTION98
4.2936-5.40840.17651470.12782710X-RAY DIFFRACTION95
5.4084-49.51450.20881380.15232707X-RAY DIFFRACTION90

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