PDB-7pgy: Structure of light-adapted AsLOV2 wild type

ID or keywords:

Entry

Database: PDB / ID: 7pgy

Title

Structure of light-adapted AsLOV2 wild type

Components

NPH1-1

Keywords

SIGNALING PROTEIN / flavin / light-oxygen-voltage /

optogenetics /

photoreceptor /

phototropin

Function / homology

Function and homology information

blue light photoreceptor activity /

non-specific serine/threonine protein kinase /

protein kinase activity /

phosphorylation /

ATP binding /

metal ion binding
Similarity search - Function

Biological species

Avena sativa (oats)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.09 Å

Authors

Gelfert, R. / Weyand, M. / Moeglich, A.

Funding support

Germany, 1items

Citation

Journal: Nat Commun / Year: 2022
Title: Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine.
Authors: Dietler, J. / Gelfert, R. / Kaiser, J. / Borin, V. / Renzl, C. / Pilsl, S. / Ranzani, A.T. / Garcia de Fuentes, A. / Gleichmann, T. / Diensthuber, R.P. / Weyand, M. / Mayer, G. / Schapiro, I. / Moglich, A.

History

Deposition	Aug 16, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 11, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 25, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7pgy.cif.gz	111.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7pgy.ent.gz		Display	PDB format
PDBx/mmJSON format	7pgy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pg/7pgy ftp://data.pdbj.org/pub/pdb/validation_reports/pg/7pgy	HTTPS FTP

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Related structure data

Related structure data	7pgxC 7pgzC 7ph0C 2v0uS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (6) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (2) #207 - Mar 2017 Photoactive Yellow Protein similarity (5) #122 - Feb 2010 Enhanceosome similarity (2)

Deposited unit

AAA: NPH1-1

hetero molecules

18.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	35.610, 56.010, 66.520
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules AAA

#1: Protein	NPH1-1 Mass: 16853.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Avena sativa (oats) / Gene: NPH1-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CmpX13 / References: UniProt: O49003

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Non-polymers , 7 types, 210 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.97 Å³/Da / Density % sol: 37.5 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 0.1 M sodium acetate pH 4.6-5.0, 6-8% (w/v) PEG 4000, 30% (v/v) glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2020
Radiation	Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.09→42.845 Å / Num. obs: 55866 / % possible obs: 99.2 % / Redundancy: 7 % / CC_1/2: 0.999 / Net I/σ(I): 12
Reflection shell	Resolution: 1.09→1.16 Å / Redundancy: 6.2 % / Num. unique obs: 8789 / CC_1/2: 0.45 / % possible all: 98

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
pointless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2v0u

2v0u

Resolution: 1.09→42.845 Å / Cor.coef. F_o:F_c: 0.987 / Cor.coef. F_o:F_c free: 0.976 / WR_factor R_free: 0.145 / WR_factor R_work: 0.107 / SU B: 2.085 / SU ML: 0.038 / Average fsc free: 0.8499 / Average fsc work: 0.8664 / Cross valid method: FREE R-VALUE / ESU R: 0.034 / ESU R Free: 0.036
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1612	2100	3.759 %
R_work	0.1226	53766	-
all	0.124	-	-
obs	-	55866	99.217 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 16.033 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.553 Å²	0 Å²	0 Å²
2-	-	2.004 Å²	-0 Å²
3-	-	-	-1.451 Å²

Refinement step

Cycle: LAST / Resolution: 1.09→42.845 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1186	0	89	195	1470

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	1964
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1868
X-RAY DIFFRACTION	r_angle_refined_deg	1.821	1.668	2692
X-RAY DIFFRACTION	r_angle_other_deg	1.447	1.595	4353
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.121	5	247
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.19	22.661	124
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.813	15	365
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.137	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	258
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	2276
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	456
X-RAY DIFFRACTION	r_nbd_refined	0.29	0.2	338
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.197	0.2	1389
X-RAY DIFFRACTION	r_nbtor_refined	0.199	0.2	654
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	687
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	159
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.103	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.241	0.2	37
X-RAY DIFFRACTION	r_nbd_other	0.199	0.2	134
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.231	0.2	41
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.108	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.073	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.599	1.332	868
X-RAY DIFFRACTION	r_mcbond_other	1.499	1.323	864
X-RAY DIFFRACTION	r_mcangle_it	1.838	2	1107
X-RAY DIFFRACTION	r_mcangle_other	1.837	2.001	1108
X-RAY DIFFRACTION	r_scbond_it	2.531	1.653	1096
X-RAY DIFFRACTION	r_scbond_other	2.535	1.653	1089
X-RAY DIFFRACTION	r_scangle_it	2.687	2.362	1562
X-RAY DIFFRACTION	r_scangle_other	2.687	2.361	1563
X-RAY DIFFRACTION	r_lrange_it	3.214	16.519	2068
X-RAY DIFFRACTION	r_lrange_other	3.002	15.814	2023
X-RAY DIFFRACTION	r_rigid_bond_restr	3.023	3	3819

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.09-1.118	0.387	151	0.328	3869	0.33	4111	0.51	0.599	97.7864	0.323
1.118-1.149	0.281	148	0.299	3789	0.298	4009	0.549	0.594	98.204	0.288
1.149-1.182	0.254	143	0.269	3683	0.269	3881	0.701	0.718	98.5828	0.254
1.182-1.218	0.263	142	0.255	3619	0.255	3807	0.715	0.75	98.7917	0.236
1.218-1.258	0.265	136	0.226	3480	0.227	3658	0.832	0.827	98.8518	0.204
1.258-1.302	0.23	133	0.199	3413	0.2	3571	0.88	0.878	99.2999	0.172
1.302-1.352	0.197	128	0.174	3273	0.175	3418	0.903	0.9	99.5026	0.147
1.352-1.407	0.189	123	0.161	3164	0.162	3308	0.889	0.91	99.3652	0.13
1.407-1.469	0.17	120	0.124	3064	0.126	3197	0.948	0.951	99.5934	0.098
1.469-1.541	0.147	114	0.1	2911	0.102	3034	0.966	0.97	99.7034	0.077
1.541-1.624	0.143	109	0.08	2806	0.082	2921	0.97	0.981	99.7946	0.062
1.624-1.722	0.131	103	0.066	2634	0.069	2745	0.979	0.987	99.7086	0.053
1.722-1.841	0.129	98	0.067	2499	0.07	2601	0.978	0.988	99.8462	0.056
1.841-1.988	0.123	91	0.072	2335	0.074	2433	0.982	0.988	99.7123	0.065
1.988-2.178	0.108	84	0.071	2135	0.072	2225	0.986	0.991	99.7303	0.066
2.178-2.434	0.124	76	0.085	1966	0.086	2047	0.982	0.987	99.7557	0.085
2.434-2.809	0.122	69	0.09	1749	0.092	1825	0.981	0.986	99.6164	0.094
2.809-3.436	0.112	58	0.103	1483	0.103	1541	0.984	0.985	100	0.113
3.436-4.844	0.141	46	0.108	1188	0.109	1235	0.983	0.986	99.919	0.132
4.844-42.845	0.297	28	0.203	706	0.207	740	0.943	0.959	99.1892	0.251

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Protein , 1 types, 1 molecules AAA

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