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- PDB-8a4e: Room temperature structure of AtPhot2LOV2 in a photostationary eq... -

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Basic information

Entry
Database: PDB / ID: 8a4e
TitleRoom temperature structure of AtPhot2LOV2 in a photostationary equilibrium
ComponentsPhototropin-2
KeywordsPLANT PROTEIN / LOV domain
Function / homology
Function and homology information


chloroplast relocation / phototropism / stomatal movement / blue light photoreceptor activity / response to blue light / plastid / circadian rhythm / kinase activity / FMN binding / protein autophosphorylation ...chloroplast relocation / phototropism / stomatal movement / blue light photoreceptor activity / response to blue light / plastid / circadian rhythm / kinase activity / FMN binding / protein autophosphorylation / 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 / PAS repeat profile. / PAS domain / PAS domain superfamily / Serine/threonine-protein kinase, active site ...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 / 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
Similarity search - Domain/homology
6-(3-TETRADECANOIC ACID) FLAVINE MONONUCLEOTIDE / FLAVIN MONONUCLEOTIDE / Phototropin-2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsEngilberge, S. / Caramello, N. / Royant, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Iucrj / Year: 2022
Title: Slow protein dynamics probed by time-resolved oscillation crystallography at room temperature.
Authors: Aumonier, S. / Engilberge, S. / Caramello, N. / von Stetten, D. / Gotthard, G. / Leonard, G.A. / Mueller-Dieckmann, C. / Royant, A.
History
DepositionJun 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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
A: Phototropin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1473
Polymers15,0081
Non-polymers1,1392
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.555, 41.555, 132.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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 protein 1


Mass: 15007.909 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHOT2, CAV1, KIN7, NPL1, At5g58140, K21L19.6 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P93025, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-FMA / 6-(3-TETRADECANOIC ACID) FLAVINE MONONUCLEOTIDE


Mass: 682.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H47N4O11P
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.91 Å3/Da / Density % sol: 35.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES pH 6.0, 4 to 9 % PEG8000, and 50 to 200 mM calcium acetate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.96→39.66 Å / Num. obs: 7757 / % possible obs: 91.9 % / Redundancy: 8.4 % / CC1/2: 0.98 / Rpim(I) all: 0.082 / Net I/σ(I): 5.7
Reflection shellResolution: 1.96→2.08 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3612 / CC1/2: 0.67 / Rpim(I) all: 0.564

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QQK

6qqk


Resolution: 1.96→35.23 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 354 4.56 %
Rwork0.1872 7402 -
obs0.1889 7756 85.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.09 Å2 / Biso mean: 42.3896 Å2 / Biso min: 17.82 Å2
Refinement stepCycle: final / Resolution: 1.96→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms888 0 62 47 997
Biso mean--28.11 47.51 -
Num. residues----107
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-2.240.294850.25951541162656
2.24-2.820.2791180.234628472965100
2.82-35.230.20251510.164530143165100

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