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- PDB-8a2v: Room temperature structure of the ground state of AtPhot2LOV2 in ... -

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Basic information

Entry
Database: PDB / ID: 8a2v
TitleRoom temperature structure of the ground state of AtPhot2LOV2 in space group P43212
ComponentsPhototropin-2
KeywordsPLANT PROTEIN / LOV domain
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 / 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
FLAVIN MONONUCLEOTIDE / Phototropin-2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 6, 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

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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)15,6593
Polymers15,0081
Non-polymers6522
Water1,62190
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)40.829, 40.829, 132.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1187-

HOH

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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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.84 Å3/Da / Density % sol: 33.3 %
Crystal growTemperature: 298 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: 298 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: 1.58→34.78 Å / Num. obs: 14046 / % possible obs: 92.1 % / Redundancy: 8 % / CC1/2: 0.99 / Rpim(I) all: 0.071 / Net I/σ(I): 6.3
Reflection shellResolution: 1.59→1.64 Å / % possible obs: 46.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 297 / CC1/2: 0.58 / Rpim(I) all: 0.537

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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: 1.59→30.01 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1996 --
Rwork0.165 --
obs-13978 92.1 %
Displacement parametersBiso max: 120.98 Å2 / Biso mean: 23.7295 Å2 / Biso min: 7.93 Å2
Refinement stepCycle: LAST / Resolution: 1.59→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 43 90 1088

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