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- PDB-2z6c: Crystal structure of LOV1 domain of phototropin1 from Arabidopsis... -

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Basic information

Entry
Database: PDB / ID: 2z6c
TitleCrystal structure of LOV1 domain of phototropin1 from Arabidopsis thaliana
ComponentsPhototropin-1
KeywordsTRANSFERASE / PAS-FOLD / LOV-FOLD / ATP-binding / Chromophore / Cytoplasm / Flavoprotein / FMN / Kinase / Membrane / Nucleotide-binding / Phosphorylation / Photoreceptor protein / Receptor / Sensory transduction / Serine/threonine-protein kinase
Function / homology
Function and homology information


chloroplast avoidance movement / chloroplast accumulation movement / cellular response to blue light / regulation of proton transport / phototropism / regulation of stomatal movement / blue light photoreceptor activity / response to blue light / plant-type vacuole / circadian rhythm ...chloroplast avoidance movement / chloroplast accumulation movement / cellular response to blue light / regulation of proton transport / phototropism / regulation of stomatal movement / blue light photoreceptor activity / response to blue light / plant-type vacuole / circadian rhythm / cytoplasmic side of plasma membrane / kinase activity / FMN binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / mRNA binding / cell surface / ATP binding / identical protein binding / cytoplasm
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-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phototropin-1
B: Phototropin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3114
Polymers28,3982
Non-polymers9132
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-28.5 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.150, 64.920, 70.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phototropin-1 / Non-phototropic hypocotyl protein 1 / Root phototropism protein 1


Mass: 14199.078 Da / Num. of mol.: 2 / Fragment: UNP residues 180-308, LOV1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHOT1, JK224, NPH1, RPT1 / Production host: Escherichia coli (E. coli)
References: UniProt: O48963, 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.: 140 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, pH8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 22, 2007 / Details: monochrometer/focusing mirror
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16967 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 13.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 41.8
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4.8 / % 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: 2.1→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.128 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24278 855 5.1 %RANDOM
Rwork0.18892 ---
obs0.19169 16014 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.54 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2--0.21 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 62 140 2080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221979
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.9932680
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3455240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76424.76284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54115336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.965158
X-RAY DIFFRACTIONr_chiral_restr0.1330.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021456
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.2857
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21361
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2881.51238
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.03921918
X-RAY DIFFRACTIONr_scbond_it2.6263934
X-RAY DIFFRACTIONr_scangle_it3.894.5762
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 54 -
Rwork0.183 1110 -
obs--97.49 %

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