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- PDB-7aby: Crystal structure of iLOV-Q489K mutant -

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Basic information

Entry
Database: PDB / ID: 7aby
TitleCrystal structure of iLOV-Q489K mutant
ComponentsPhototropin-2
KeywordsSIGNALING PROTEIN / LOV domain / BLUE LIGHT PHOTORECEPTOR / FLAVOPROTEIN
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
ACETATE ION / FLAVIN MONONUCLEOTIDE / Phototropin-2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsGranzin, J. / Batra-Safferling, R.
Citation
Journal: J.Biol.Chem. / Year: 2021
Title: The molecular basis of spectral tuning in blue- and red-shifted flavin-binding fluorescent proteins.
Authors: Rollen, K. / Granzin, J. / Remeeva, A. / Davari, M.D. / Gensch, T. / Nazarenko, V.V. / Kovalev, K. / Bogorodskiy, A. / Borshchevskiy, V. / Hemmer, S. / Schwaneberg, U. / Gordeliy, V. / ...Authors: Rollen, K. / Granzin, J. / Remeeva, A. / Davari, M.D. / Gensch, T. / Nazarenko, V.V. / Kovalev, K. / Bogorodskiy, A. / Borshchevskiy, V. / Hemmer, S. / Schwaneberg, U. / Gordeliy, V. / Jaeger, K.E. / Batra-Safferling, R. / Gushchin, I. / Krauss, U.
#1: Journal: Biorxiv / Year: 2021
Title: Structural and mechanistic insight into spectral tuning in flavin-binding fluorescent proteins
Authors: Rollen, K. / Granzin, J. / Remeeva, A. / Davari, M.D. / Gensch, T. / Nazarenko, V.V. / Kovalev, K. / Bogorodskiy, A. / Borshchevskiy, V. / Hemmer, S. / Schwaneberg, U. / Gordeliy, V. / ...Authors: Rollen, K. / Granzin, J. / Remeeva, A. / Davari, M.D. / Gensch, T. / Nazarenko, V.V. / Kovalev, K. / Bogorodskiy, A. / Borshchevskiy, V. / Hemmer, S. / Schwaneberg, U. / Gordeliy, V. / Jaeger, K.E. / Batra-Safferling, R. / Gushchin, I. / Krauss, U.
History
DepositionSep 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0Jul 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_peptide_omega / pdbx_validate_rmsd_bond / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_validate_rmsd_bond.auth_comp_id_1
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 3.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.2Oct 9, 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)15,5613
Polymers15,0461
Non-polymers5152
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-4 kcal/mol
Surface area6280 Å2
Unit cell
Length a, b, c (Å)40.756, 40.756, 131.791
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-687-

HOH

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Components

#1: Protein Phototropin-2 / Defective in chloroplast avoidance protein 1 / Non-phototropic hypocotyl 1-like protein 1 / AtKin7 ...Defective in chloroplast avoidance protein 1 / Non-phototropic hypocotyl 1-like protein 1 / AtKin7 / NPH1-like protein 1


Mass: 15045.925 Da / Num. of mol.: 1 / Mutation: D491(SNN), G492(ACY), Q489K
Source method: isolated from a genetically manipulated source
Details: modified residues: Asp491-Gly492 to SNN L-3-AMINOSUCCINIMIDE and ACY ACETIC ACID including the required backbone bonds. Asp-Gly form a Succinimide intermediate. Keyword: Deamidation
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.82 Å3/Da / Density % sol: 32.56 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate, 25 % (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9194 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 1.45→43.93 Å / Num. obs: 20710 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 19.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.025 / Rrim(I) all: 0.074 / Net I/σ(I): 14.3 / Num. measured all: 186700
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.489.61.107984710300.7750.3761.172.1100
7.81-43.936.80.03212951900.9990.0130.03538.199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.482
Highest resolutionLowest resolution
Rotation38.94 Å1.78 Å

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Processing

Software
NameVersionClassification
XDSVERSION Jun 1, 2017 BUILT=20170601data reduction
Aimless0.5.32data scaling
MOLREPVers 11.5.05; 04.08.2017phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EES

4ees


Resolution: 1.45→38.937 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1847 958 4.64 %
Rwork0.1563 19671 -
obs0.1576 20629 99.99 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.3 Å2 / Biso mean: 24.9037 Å2 / Biso min: 12.97 Å2
Refinement stepCycle: final / Resolution: 1.45→38.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms875 0 35 106 1016
Biso mean--16.55 36.57 -
Num. residues----107
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4501-1.52650.23561360.17222728
1.5265-1.62220.24431500.16242723
1.6222-1.74740.2111430.15732759
1.7474-1.92330.1861240.14712784
1.9233-2.20160.20041350.14062779
2.2016-2.77360.20221240.15922870
2.7736-38.9371460.15633028

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