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- PDB-6wle: Crystal structure of the Zeitlupe light-state mimic G46A -

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Basic information

Entry
Database: PDB / ID: 6wle
TitleCrystal structure of the Zeitlupe light-state mimic G46A
ComponentsAdagio protein 1
KeywordsPLANT PROTEIN / Circadian clock control / dimer
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. / Galactose oxidase/kelch, beta-propeller / F-box-like domain superfamily / 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. / Galactose oxidase/kelch, beta-propeller / F-box-like domain superfamily / F-box-like / F-box domain / PAS domain / Kelch-type beta propeller / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Adagio protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZoltowski, B. / Green, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R15GM109282 United States
CitationJournal: Biochemistry / Year: 2021
Title: Steric and Electronic Interactions at Gln154 in ZEITLUPE Induce Reorganization of the LOV Domain Dimer Interface.
Authors: Pudasaini, A. / Green, R. / Song, Y.H. / Blumenfeld, A. / Karki, N. / Imaizumi, T. / Zoltowski, B.D.
History
DepositionApr 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
E: Adagio protein 1
F: Adagio protein 1
G: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,08817
Polymers145,7087
Non-polymers3,38110
Water1,838102
1
B: Adagio protein 1
D: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6065
Polymers41,6312
Non-polymers9753
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-23 kcal/mol
Surface area14260 Å2
MethodPISA
2
A: Adagio protein 1
E: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6065
Polymers41,6312
Non-polymers9753
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-23 kcal/mol
Surface area14290 Å2
MethodPISA
3
C: Adagio protein 1
G: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6065
Polymers41,6312
Non-polymers9753
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-21 kcal/mol
Surface area14190 Å2
MethodPISA
4
F: Adagio protein 1
hetero molecules

F: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5434
Polymers41,6312
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_455-x-1/2,y,-z1
Buried area3740 Å2
ΔGint-26 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.822, 265.822, 265.822
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11F-17-

CYS

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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: 20815.404 Da / Num. of mol.: 7 / Mutation: G46A
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 / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 5.37 Å3/Da / Density % sol: 77.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES pH 6.0, 1.6 M Ammonium Sulfate, 0.01 M Cobalt Chloride Hexahydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9773 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9773 Å / Relative weight: 1
ReflectionResolution: 3→45.59 Å / Num. obs: 62237 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 53.42 Å2 / Rmerge(I) obs: 0.172 / Net I/σ(I): 17.5
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 3079 / CC1/2: 0.642

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SVU

5svu


Resolution: 3→45.59 Å / SU ML: 0.396 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1092
RfactorNum. reflection% reflection
Rfree0.2425 1997 3.21 %
Rwork0.2029 --
obs0.2041 62142 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.57 Å2
Refinement stepCycle: LAST / Resolution: 3→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7243 0 229 102 7574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01737631
X-RAY DIFFRACTIONf_angle_d1.558710375
X-RAY DIFFRACTIONf_chiral_restr0.07011157
X-RAY DIFFRACTIONf_plane_restr0.00891328
X-RAY DIFFRACTIONf_dihedral_angle_d18.42171049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.32341400.29694283X-RAY DIFFRACTION99.93
3.08-3.160.34581440.28514275X-RAY DIFFRACTION99.86
3.16-3.250.32311440.27064277X-RAY DIFFRACTION99.77
3.25-3.360.32991450.25874264X-RAY DIFFRACTION99.95
3.36-3.480.2841380.26964268X-RAY DIFFRACTION99.86
3.48-3.610.27671450.21864267X-RAY DIFFRACTION99.91
3.62-3.780.27371460.25724237X-RAY DIFFRACTION99.3
3.78-3.980.31021390.25434274X-RAY DIFFRACTION99.59
3.98-4.230.21031440.17244307X-RAY DIFFRACTION99.98
4.23-4.550.20071400.13824282X-RAY DIFFRACTION100
4.55-5.010.14551420.13064340X-RAY DIFFRACTION100
5.01-5.740.16841450.14894313X-RAY DIFFRACTION100
5.74-7.220.20541400.17874348X-RAY DIFFRACTION100
7.22-45.590.24221450.19384410X-RAY DIFFRACTION98.89

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