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- PDB-6qqk: Room temperature structure of blue light-irradiated AtPhot2LOV2 r... -

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Basic information

Entry
Database: PDB / ID: 6qqk
TitleRoom temperature structure of blue light-irradiated AtPhot2LOV2 recorded after an accumulated dose of 34 kGy
ComponentsPhototropin-2
KeywordsPLANT PROTEIN / Room temperature macromolecular crystallography / cryo-crystallography / specific radiation damage / time-resolved crystallography
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 / 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: 2.4 Å
AuthorsAumonier, S. / Gotthard, G. / Royant, A.
Citation
Journal: Iucrj / Year: 2019
Title: Specific radiation damage is a lesser concern at room temperature.
Authors: Gotthard, G. / Aumonier, S. / De Sanctis, D. / Leonard, G. / von Stetten, D. / Royant, A.
#1: Journal: Iucrj / Year: 2019
Title: Specific radiation damage is a lesser concern at room temperature
Authors: Gotthard, G. / Aumonier, S. / De Sanctis, D. / Leonard, G. / von Stetten, D. / Royant, A.
History
DepositionFeb 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4642
Polymers15,0081
Non-polymers4561
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-5 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.450, 41.450, 133.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.91 Å3/Da / Density % sol: 35.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 12-17% PEG8000 0.2 M Calcium acetate 0.1 M MES

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.4→39.59 Å / Num. obs: 4926 / % possible obs: 98 % / Redundancy: 23.1 % / Biso Wilson estimate: 51.997 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.64
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 23.5 % / Mean I/σ(I) obs: 1.52 / Num. unique obs: 558 / CC1/2: 0.726 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4eep

4eep


Resolution: 2.4→39.59 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.083 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 0.843 / ESU R Free: 0.332 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28623 245 5 %RANDOM
Rwork0.23916 ---
obs0.24184 4680 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.905 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å2-0 Å2-0 Å2
2--1.82 Å2-0 Å2
3----3.64 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 31 6 877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0131069
X-RAY DIFFRACTIONr_bond_other_d0.0010.017956
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.7471466
X-RAY DIFFRACTIONr_angle_other_deg1.0071.6272220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.595.586128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.621.53865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86415177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2721510
X-RAY DIFFRACTIONr_chiral_restr0.0320.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3974.992470
X-RAY DIFFRACTIONr_mcbond_other1.3964.994468
X-RAY DIFFRACTIONr_mcangle_it2.4817.468595
X-RAY DIFFRACTIONr_mcangle_other2.4787.468596
X-RAY DIFFRACTIONr_scbond_it1.0755.028599
X-RAY DIFFRACTIONr_scbond_other1.0765.033597
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9417.436871
X-RAY DIFFRACTIONr_long_range_B_refined3.97846.7161204
X-RAY DIFFRACTIONr_long_range_B_other3.97646.7011205
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 13 -
Rwork0.322 353 -
obs--99.19 %

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