PDB-4hhd: 2.75 Angstrom resolution crystal structure of the A. thaliana LOV...

ID or keywords:

Entry

Database: PDB / ID: 4hhd

Title

2.75 Angstrom resolution crystal structure of the A. thaliana LOV2 domain with an extended N-terminal A' helix (cryo dark structure)

Components

Phototropin-1

Keywords

TRANSFERASE / LOV2 / KINASE / ATP-BINDING / ARABIDOPSIS THALIANA / SERINE/THREONINE-PROTEIN KINASE / LIGHT-INDUCED SIGNAL TRANSDUCTION / PHOTOTROPIN-1 / LOV (PAS) domain

Function / homology

Function and homology information

chloroplast avoidance movement / chloroplast accumulation movement / cellular response to blue light / regulation of proton transport / phototropism / regulation of stomatal movement / response to blue light / blue light photoreceptor activity / plant-type vacuole / cytoplasmic side of plasma membrane ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Halavaty, A.S. / Moffat, K.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Coiled-coil dimerization of the LOV2 domain of the blue-light photoreceptor phototropin 1 from Arabidopsis thaliana.
Authors: Halavaty, A.S. / Moffat, K.

History

Deposition	Oct 9, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Dec 11, 2013	Group: Database references
Revision 1.2	Feb 12, 2014	Group: Database references
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4hhd.cif.gz	146 KB	Display	PDBx/mmCIF format
PDB format	pdb4hhd.ent.gz	115.1 KB	Display	PDB format
PDBx/mmJSON format	4hhd.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/hh/4hhd ftp://data.pdbj.org/pub/pdb/validation_reports/hh/4hhd	HTTPS FTP

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Related structure data

Related structure data	2v0uS S: Starting model for refinement
Similar structure data	4qpc-d 4l8k-3 2cfi-d 4ts4-d 6lkb-d 3lzw-d 4r8v-d 3f9e-d 4cua-d 3zrj-d Search similar-shape structures by Omokage search (details) 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 (7) #207 - Mar 2017 Photoactive Yellow Protein similarity (6) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (2) #122 - Feb 2010 Enhanceosome similarity (2)

Deposited unit

A: Phototropin-1

B: Phototropin-1

hetero molecules

39.2 kDa, 2 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)	63.382, 63.382, 171.318
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Phototropin-1 / Non-phototropic hypocotyl protein 1 / Root phototropism protein 1 Mass: 19119.664 Da / Num. of mol.: 2 / Fragment: UNP residues 452-615 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHOT1, JK224, NPH1, RPT1, At3g45780, T6D9_110 / Plasmid: pET-28c(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O48963, 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: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.33 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: Protein at 21 mg/mL in 20 mM TRIS-HCl pH 7.4, 20 mM NaCl, 15 % glycerol Crystallization: The JCSG+ Suite (D12: 0.04 M Potassium phosphate, 16% (w/v) PEG 8000, 20% (v/v) glycerol), VAPOR ...Details: Protein at 21 mg/mL in 20 mM TRIS-HCl pH 7.4, 20 mM NaCl, 15 % glycerol Crystallization: The JCSG+ Suite (D12: 0.04 M Potassium phosphate, 16% (w/v) PEG 8000, 20% (v/v) glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 287K

Crystal

Density Matthews: 2.25 Å³/Da / Density % sol: 45.33 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Protein at 21 mg/mL in 20 mM TRIS-HCl pH 7.4, 20 mM NaCl, 15 % glycerol Crystallization: The JCSG+ Suite (D12: 0.04 M Potassium phosphate, 16% (w/v) PEG 8000, 20% (v/v) glycerol), VAPOR ...

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Data collection

Diffraction	Mean temperature: 105 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2007 / Details: Bent conical Si-mirror (Rh coated)
Radiation	Monochromator: BENT GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9002 Å / Relative weight: 1
Reflection	Resolution: 2.75→30 Å / Num. all: 8574 / Num. obs: 8574 / % possible obs: 87.9 % / Observed criterion σ(F): -3 / Redundancy: 3.3 % / B_iso Wilson estimate: 66.3 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 17.5
Reflection shell	Resolution: 2.75→2.8 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.585 / Mean I/σ(I) obs: 2.2 / Num. unique all: 399 / % possible all: 86.6

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V0U

2v0u

Resolution: 2.75→29.72 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.879 / SU B: 41.796 / SU ML: 0.369 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2894	417	4.9 %	RANDOM
R_work	0.23109	-	-	-
obs	0.23399	8128	88.18 %	-
all	-	8128	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 48.442 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.75 Å²	0 Å²	0 Å²
2-	-	-1.75 Å²	-0 Å²
3-	-	-	3.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→29.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2466	0	63	29	2558

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	2598
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1802
X-RAY DIFFRACTION	r_angle_refined_deg	1.312	1.999	3512
X-RAY DIFFRACTION	r_angle_other_deg	0.849	3	4399
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.771	5	306
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	23.087	24.809	131
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.903	15	495
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.057	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	393
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2822
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	496
X-RAY DIFFRACTION	r_mcbond_it	0.421	1.5	1529
X-RAY DIFFRACTION	r_mcbond_other	0.065	1.5	618
X-RAY DIFFRACTION	r_mcangle_it	0.8	2	2496
X-RAY DIFFRACTION	r_scbond_it	1.071	3	1069
X-RAY DIFFRACTION	r_scangle_it	1.787	4.5	1016

LS refinement shell

Resolution: 2.75→2.821 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.472	39	-
R_work	0.297	545	-
obs	-	545	85.51 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	19.1089	1.7339	-12.643	0.6352	-7.3261	36.6531	-0.3205	1.0314	-0.641	0.0291	-0.0548	-0.0526	-0.6429	0.2707	0.3752	0.3664	-0.0656	-0.0064	0.2355	0.0123	0.2743	36.7056	11.8842	1.3891
2	1.2346	0.4993	-0.8254	2.2651	0.0774	0.6563	-0.1175	-0.0495	-0.1834	-0.1882	-0.0591	0.0477	0.1619	0.1035	0.1767	0.1844	0.0963	0.0399	0.1138	0.0284	0.0408	23.5097	2.3835	12.1562
3	4.8954	0.5362	1.9611	6.8577	-3.3417	8.0032	0.355	0.0121	0.1065	-0.2016	-0.2549	-0.4728	0.5562	0.0288	-0.1001	0.0726	0.0213	0.0098	0.0263	0.025	0.0729	24.2902	-7.313	15.7487
4	3.0927	1.8851	-2.6274	2.7474	-0.4773	2.9934	-0.2065	0.2349	0.0188	-0.3108	0.0842	0.2434	0.0387	-0.2513	0.1223	0.117	-0.0169	-0.0447	0.0396	-0.0311	0.1087	8.4262	-12.5391	14.8606
5	6.8405	0.3147	1.9892	-0.7402	-1.4183	6.8248	-0.1603	0.5397	0.4665	-0.1191	0.1886	0.1477	0.0605	-0.6012	-0.0283	0.313	0.0046	-0.0895	0.1336	0.0515	0.2159	5.708	-2.6321	7.5697
6	4.1524	0.491	-0.9692	6.0459	-4.5389	8.7959	0.2916	0.4461	0.1619	0.1267	0.2436	0.7004	-0.2271	-0.5212	-0.5352	0.1009	0.0118	0.022	0.0961	0.0073	0.0926	12.6071	-3.4084	15.4412
7	6.7785	-0.0798	0.7864	6.1837	-2.471	-0.3415	-0.0971	-0.0554	0.1708	0.5296	0.073	-0.0643	-0.3116	-0.118	0.0241	0.3315	0.05	-0.012	0.0262	-0.0448	0.1323	14.6454	-0.3966	15.8621
8	3.9884	5.7668	-13.2804	2.7659	-13.1702	20.636	0.2575	0.8773	-0.1005	0.7659	0.4666	0.3262	-1.3123	-2.0178	-0.7241	0.4025	0.0261	0.1418	0.6584	-0.1234	0.8794	5.0978	5.2185	25.2308
9	7.9756	-0.5392	-3.4866	5.9864	-2.275	10.5708	0.23	0.247	0.2003	-0.0188	0.1116	-0.0047	-0.4013	-0.2015	-0.3415	0.0499	0.0491	-0.0033	0.0703	-0.006	0.0342	17.5311	9.9542	13.4975
10	-2.6945	-8.5377	-3.8845	48.3993	5.7891	-2.4485	-0.1704	-0.2915	-0.4679	-2.2588	-0.3131	0.8701	-0.1234	0.3541	0.4835	0.5715	0.1984	0.2242	0.4684	0.1768	0.3879	12.0259	-7.9438	11.3396
11	-0.0653	1.6336	-1.615	11.9031	-14.8937	15.5543	-0.3879	0.8979	0.4821	-0.2937	-0.3029	-0.7201	0.2956	-0.0706	0.6909	0.4985	-0.1863	-0.0407	1.0369	0.2708	0.3738	27.8623	3.3777	1.1011
12	7.4327	-0.5188	0.5035	-0.2424	0.7541	1.072	0.0745	-0.511	-0.5574	-0.1746	-0.0253	-0.0037	-0.1779	-0.1203	-0.0493	0.2328	0.037	0.1113	0.1338	0.0335	0.1144	38.9732	4.1208	13.918
13	4.0468	-0.4359	-0.106	-0.3887	0.6337	2.3462	0.0362	-0.2726	-0.0345	0.062	0.0693	-0.0285	0.0753	0.0024	-0.1056	0.1335	0.0496	0.0649	0.2044	0.014	0.108	38.1983	8.0026	23.6597
14	10.7231	-2.6763	5.2329	0.4813	-1.3146	2.6206	-0.1176	-0.3591	0.072	0.0987	0.1061	-0.1055	-0.2047	-0.0484	0.0115	0.2657	0.0419	-0.0491	0.2979	-0.066	0.3684	51.2141	12.1663	27.6154
15	10.8908	13.538	3.2614	17.1842	1.5289	-0.3852	-0.0858	-0.4638	0.4204	0.0841	-0.3583	-1.0316	-0.0301	-0.2601	0.4441	0.0807	0.0279	-0.0038	0.4875	-0.0261	0.7924	56.3925	13.4848	15.328
16	5.4324	3.1634	-2.3485	1.8507	-3.0372	6.5065	-0.1531	-0.3162	-0.0396	0.0283	-0.1601	-0.2478	0.4031	-0.024	0.3132	0.458	0.0779	-0.0232	0.442	0.0271	0.2777	48.8772	3.9164	32.1839
17	0.6291	0.4267	-0.9588	5.6139	-2.1084	5.4445	0.0724	0.0431	0.0897	-0.2014	-0.1705	-0.3377	-0.2701	0.4298	0.0981	0.0946	-0.0079	0.1283	0.2505	0.0497	0.1867	49.0447	7.8953	12.6716
18	9.8503	-6.267	6.653	5.1426	-4.453	4.7698	-0.1275	-0.2113	-0.0366	0.0691	0.0006	-0.1314	-0.3139	-0.1336	0.1269	0.2629	0.0431	0.0908	0.189	-0.0258	0.3815	58.0143	-7.3948	23.6159
19	22.4248	6.7574	4.1545	5.7223	1.6841	0.1775	0.3539	1.7002	-0.3958	-1.5042	-0.362	-0.1746	0.5478	0.3164	0.0081	1.0609	0.3437	0.2157	0.3911	0.0515	0.3515	44.7528	-0.1438	7.4013
20	-4.6657	-0.8934	-4.0541	3.7712	4.8212	28.8144	0.089	-0.114	-0.0071	0.1578	-0.5993	0.2025	-1.3708	-0.9307	0.5103	0.0627	0.0276	-0.0365	0.5807	-0.009	0.4654	49.8708	12.0586	22.0922

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	452 - 463
2	X-RAY DIFFRACTION	2	A	464 - 486
3	X-RAY DIFFRACTION	3	A	487 - 510
4	X-RAY DIFFRACTION	4	A	511 - 527
5	X-RAY DIFFRACTION	5	A	528 - 540
6	X-RAY DIFFRACTION	6	A	541 - 567
7	X-RAY DIFFRACTION	7	A	568 - 580
8	X-RAY DIFFRACTION	8	A	593 - 599
9	X-RAY DIFFRACTION	9	A	600 - 615
10	X-RAY DIFFRACTION	10	A	701
11	X-RAY DIFFRACTION	11	B	458 - 465
12	X-RAY DIFFRACTION	12	B	466 - 484
13	X-RAY DIFFRACTION	13	B	485 - 507
14	X-RAY DIFFRACTION	14	B	508 - 528
15	X-RAY DIFFRACTION	15	B	529 - 538
16	X-RAY DIFFRACTION	16	B	539 - 552
17	X-RAY DIFFRACTION	17	B	553 - 576
18	X-RAY DIFFRACTION	18	B	577 - 602
19	X-RAY DIFFRACTION	19	B	603 - 614
20	X-RAY DIFFRACTION	20	B	701

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