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- PDB-6wlp: Crystal Structure of the ZTL light-state mimic G46S -

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Basic information

Entry
Database: PDB / ID: 6wlp
TitleCrystal Structure of the ZTL light-state mimic G46S
ComponentsAdagio protein 1
KeywordsCIRCADIAN CLOCK PROTEIN / PLANT 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)149,32519
Polymers145,8207
Non-polymers3,50512
Water1,56787
1
B: Adagio protein 1
D: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7006
Polymers41,6632
Non-polymers1,0374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-25 kcal/mol
Surface area14260 Å2
MethodPISA
2
A: Adagio protein 1
E: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7006
Polymers41,6632
Non-polymers1,0374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-22 kcal/mol
Surface area14220 Å2
MethodPISA
3
C: Adagio protein 1
G: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5754
Polymers41,6632
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-24 kcal/mol
Surface area14280 Å2
MethodPISA
4
F: Adagio protein 1
hetero molecules

F: Adagio protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7006
Polymers41,6632
Non-polymers1,0374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_455-x-1/2,y,-z1
Buried area4100 Å2
ΔGint-23 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.069, 265.069, 265.069
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

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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: 20831.404 Da / Num. of mol.: 7 / Mutation: G18S, G52R
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.: 7 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 5.32 Å3/Da / Density % sol: 76.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.05 M TRIS pH 8.5, 2.0 M Ammonium sulfate

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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→46.86 Å / Num. obs: 61739 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 59.15 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 2.95
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 3080 / CC1/2: 0.699

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Processing

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

5svu


Resolution: 3→46.86 Å / SU ML: 0.402 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8466
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 2003 3.25 %
Rwork0.1933 59690 -
obs0.1942 61693 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.14 Å2
Refinement stepCycle: LAST / Resolution: 3→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7257 0 237 87 7581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01627653
X-RAY DIFFRACTIONf_angle_d1.601410398
X-RAY DIFFRACTIONf_chiral_restr0.06761158
X-RAY DIFFRACTIONf_plane_restr0.0091329
X-RAY DIFFRACTIONf_dihedral_angle_d18.0251052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.37331440.31824292X-RAY DIFFRACTION99.89
3.08-3.160.35771440.30184207X-RAY DIFFRACTION99.91
3.16-3.250.31381400.26364201X-RAY DIFFRACTION99.86
3.25-3.360.29511420.26264268X-RAY DIFFRACTION100
3.36-3.480.30341400.24444214X-RAY DIFFRACTION99.95
3.48-3.610.23611470.21414242X-RAY DIFFRACTION99.95
3.62-3.780.25691430.19534233X-RAY DIFFRACTION100
3.78-3.980.21791430.1894252X-RAY DIFFRACTION100
3.98-4.230.20881370.17184256X-RAY DIFFRACTION99.98
4.23-4.550.14391450.13524267X-RAY DIFFRACTION99.98
4.56-5.010.14781410.13274288X-RAY DIFFRACTION100
5.01-5.740.17911380.15434295X-RAY DIFFRACTION100
5.74-7.220.19581490.1764310X-RAY DIFFRACTION100
7.22-46.860.22611500.20274365X-RAY DIFFRACTION98.99

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