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- PDB-2z6d: Crystal structure of LOV1 domain of phototropin2 from Arabidopsis... -

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Basic information

Entry
Database: PDB / ID: 2z6d
TitleCrystal structure of LOV1 domain of phototropin2 from Arabidopsis thaliana
ComponentsPhototropin-2
KeywordsTRANSFERASE / PAS-fold / LOV-fold / Alternative splicing / ATP-binding / Chromophore / Flavoprotein / FMN / Kinase / Membrane / Nucleotide-binding / Phosphorylation / Photoreceptor protein / Receptor / Sensory transduction / Serine/threonine-protein kinase
Function / homology
Function and homology information


chloroplast relocation / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / kinase activity / FMN binding / protein autophosphorylation ...chloroplast relocation / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / kinase activity / FMN binding / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain ...PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Phototropin-2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNakasako, M. / Matsuoka, D. / Tokutomi, S.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2
Authors: Nakasako, M. / Zikihara, K. / Matsuoka, D. / Katsura, H. / Tokutomi, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary X-ray diffraction analysis of the LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana
Authors: Nakasako, M. / Hirata, M. / Shimizu, N. / Hosokawa, S. / Matsuoka, D. / Oka, T. / Yamamoto, M. / Tokutomi, S.
#2: Journal: Biochemistry / Year: 2004
Title: Light-induced structural changes of LOV domain-containing polypeptides from Arabidopsis phototropin 1 and 2 studied by small-angle X-ray scattering
Authors: Nakasako, M. / Iwata, T. / Matsuoka, D. / Tokutomi, S.
#3: Journal: FEBS Lett. / Year: 2005
Title: Quaternary structure of LOV-domain containing polypeptide of Arabidopsis FKF1 protein
Authors: Nakasako, M. / Matsuoka, D. / Zikihara, K. / Tokutomi, S.
History
DepositionJul 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phototropin-2
B: Phototropin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0544
Polymers29,1412
Non-polymers9132
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-32.5 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.52, 66.51, 56.69
Angle α, β, γ (deg.)90.00, 92.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phototropin-2 / Defective in chloroplast avoidance protein 1 / Non-phototropic hypocotyl 1-like protein 1 / NPH1- ...Defective in chloroplast avoidance protein 1 / Non-phototropic hypocotyl 1-like protein 1 / NPH1-like 1 / AtKin7


Mass: 14570.555 Da / Num. of mol.: 2 / Fragment: UNP residues 117-246, LOV1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHOT2, CAV1, KIN7, NPL1 / Production host: Escherichia coli (E. coli)
References: UniProt: P93025, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, Sodium acetate, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2006 / Details: monochrometer/focusing optics
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→70 Å / Num. obs: 15677 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 6.59 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N9L

1n9l


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.771 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22682 796 5.1 %RANDOM
Rwork0.17963 ---
obs0.18202 14809 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.892 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å2-2.15 Å2
2---1.52 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 62 143 1968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221865
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9952531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8125223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69724.61578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10815316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.409158
X-RAY DIFFRACTIONr_chiral_restr0.1130.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021374
X-RAY DIFFRACTIONr_nbd_refined0.20.2859
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.214
X-RAY DIFFRACTIONr_mcbond_it1.2221.51153
X-RAY DIFFRACTIONr_mcangle_it1.90321813
X-RAY DIFFRACTIONr_scbond_it2.6843898
X-RAY DIFFRACTIONr_scangle_it4.0814.5718
LS refinement shellResolution: 1.999→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 66 -
Rwork0.187 1076 -
obs--96.13 %

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