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- PDB-8a2w: Room temperature structure of the ground state of AtPhot2LOV2 in ... -

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Basic information

Entry
Database: PDB / ID: 8a2w
TitleRoom temperature structure of the ground state of AtPhot2LOV2 in space group P212121, as recovered 1620 seconds after light irradiation
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
FLAVIN MONONUCLEOTIDE / Phototropin-2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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
B: Phototropin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9294
Polymers30,0162
Non-polymers9132
Water1,74797
1
A: Phototropin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4642
Polymers15,0081
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phototropin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4642
Polymers15,0081
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.356, 43.191, 133.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 2
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.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.16 Å3/Da / Density % sol: 36.34 %
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: 2.04→34.51 Å / Num. obs: 10070 / % possible obs: 78 % / Redundancy: 4 % / CC1/2: 0.98 / Rpim(I) all: 0.089 / Net I/σ(I): 5.3
Reflection shellResolution: 2.04→2.11 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 504 / CC1/2: 0.49 / Rpim(I) all: 0.569

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QQK

6qqk


Resolution: 2.04→34.51 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 477 4.74 %
Rwork0.1801 9591 -
obs0.1818 10068 65.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.56 Å2 / Biso mean: 42.6074 Å2 / Biso min: 15.94 Å2
Refinement stepCycle: final / Resolution: 2.04→34.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 62 98 2033
Biso mean--29.48 47.53 -
Num. residues----230
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 (%)
2.04-2.340.27491160.23471961207741
2.34-2.940.25161790.22933786396578
2.94-34.510.19171820.15323844402676
Refinement TLS params.Method: refined / Origin x: 7.6951 Å / Origin y: 2.5338 Å / Origin z: 16.7292 Å
111213212223313233
T0.1415 Å20.0142 Å20.0022 Å2-0.15 Å20.0007 Å2--0.2223 Å2
L1.0203 °20.2554 °21.1158 °2-1.1282 °20.6755 °2--3.2114 °2
S0.0092 Å °-0.0275 Å °0.0706 Å °0.0489 Å °-0.0144 Å °0.0051 Å °-0.0521 Å °0.0207 Å °-0.0094 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA389 - 502
2X-RAY DIFFRACTION1allA1001
3X-RAY DIFFRACTION1allB387 - 502
4X-RAY DIFFRACTION1allB1001
5X-RAY DIFFRACTION1allS1 - 79
6X-RAY DIFFRACTION1allW1 - 29

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