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- PDB-7wa4: Crystal structure of GIGANTEA in complex with LKP2 -

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Basic information

Entry
Database: PDB / ID: 7wa4
TitleCrystal structure of GIGANTEA in complex with LKP2
Components
  • Adagio protein 2
  • Protein GIGANTEA
KeywordsCIRCADIAN CLOCK PROTEIN / GI / LOV domain / Flavin-mononucleotide
Function / homology
Function and homology information


positive regulation of long-day photoperiodism, flowering / temperature compensation of the circadian clock / red, far-red light phototransduction / response to far red light / flower development / response to blue light / photoreceptor activity / Cajal body / response to cold / regulation of circadian rhythm ...positive regulation of long-day photoperiodism, flowering / temperature compensation of the circadian clock / red, far-red light phototransduction / response to far red light / flower development / response to blue light / photoreceptor activity / Cajal body / response to cold / regulation of circadian rhythm / response to hydrogen peroxide / circadian rhythm / rhythmic process / cell differentiation / protein ubiquitination / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
GIGANTEA / Galactose oxidase, central domain / Galactose oxidase, central domain / Kelch repeat type 2 / Kelch motif / F-box-like domain superfamily / F-box-like / F-box domain / PAS domain / Kelch-type beta propeller ...GIGANTEA / Galactose oxidase, central domain / Galactose oxidase, central domain / Kelch repeat type 2 / Kelch motif / 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 2 / Protein GIGANTEA
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsPathak, D. / Dahal, P. / Kwon, E. / Kim, D.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2022
Title: Structural analysis of the regulation of blue-light receptors by GIGANTEA.
Authors: Kwon, E. / Pathak, D. / Dahal, P. / Tandukar, S. / Jung, H.S. / Kim, W.Y. / Kim, D.Y.
History
DepositionDec 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
A: Protein GIGANTEA
B: Adagio protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2163
Polymers104,7602
Non-polymers4561
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-16 kcal/mol
Surface area30200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.750, 104.750, 232.161
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein GIGANTEA


Mass: 89438.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GI, At1g22770, T22J18.6 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q9SQI2
#2: Protein Adagio protein 2 / F-box only protein 2c / FBX2c / Flavin-binding kelch repeat F-box protein 1-like protein 1 / FKF1- ...F-box only protein 2c / FBX2c / Flavin-binding kelch repeat F-box protein 1-like protein 1 / FKF1-like protein 1 / LOV kelch protein 2


Mass: 15321.668 Da / Num. of mol.: 1 / Fragment: LKP2 LOV domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADO2, FKL1, LKP2, At2g18915, F19F24.11 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q8W420
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
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: 3.53 Å3/Da / Density % sol: 65.17 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 12% MPD, 3%(v/v) PEG 3350, 0.2M ammonium sulfate, 0.1M imidazole/HCl pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97944 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 3.5→100 Å / Num. obs: 18181 / % possible obs: 100 % / Redundancy: 9.19 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 7.7
Reflection shellResolution: 3.5→3.83 Å / Redundancy: 9.49 % / Rmerge(I) obs: 1.241 / Num. unique obs: 4311 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.5→90.72 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 0.14 / Phase error: 31.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2944 1727 10.01 %
Rwork0.2454 15526 -
obs0.2503 17253 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.22 Å2 / Biso mean: 47.4344 Å2 / Biso min: 6.71 Å2
Refinement stepCycle: final / Resolution: 3.5→90.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 31 0 4999
Biso mean--56.81 --
Num. residues----636
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.60.43861320.3521198133088
3.6-3.720.37451310.32931201133289
3.72-3.850.34861460.2911232137891
3.85-4.010.31031350.26181248138392
4.01-4.190.2891500.23471282143294
4.19-4.410.25051450.21141295144096
4.41-4.690.26761420.19951313145597
4.69-5.050.2471510.20431340149198
5.05-5.550.27061480.2211332148098
5.56-6.360.29181450.26951341148699
6.36-8.010.28371490.249913741523100
8.01-90.720.23621530.19311370152399
Refinement TLS params.Method: refined / Origin x: 16.6578 Å / Origin y: 55.9893 Å / Origin z: 62.8044 Å
111213212223313233
T0.0614 Å2-0.1855 Å2-0.095 Å2-0.003 Å2-0.0185 Å2--0.0965 Å2
L-0.0075 °2-0.0027 °2-0.0165 °2-0.0296 °20.0223 °2--0.0665 °2
S-0.0593 Å °-0.0165 Å °-0.0015 Å °-0.0219 Å °0.0082 Å °-0.0323 Å °0.1206 Å °-0.0416 Å °-0.0196 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 789
2X-RAY DIFFRACTION1allB44 - 157
3X-RAY DIFFRACTION1allC1

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