PDB-4dsc: Complex structure of abscisic acid receptor PYL3 with (+)-ABA in ...

ID or keywords:

Entry

Database: PDB / ID: 4dsc

Title

Complex structure of abscisic acid receptor PYL3 with (+)-ABA in spacegroup of H32 at 1.95A

Components

Abscisic acid receptor PYL3

Keywords

HORMONE RECEPTOR / abscisic acid receptor / ABA / pyl3

Function / homology

Function and homology information

protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Zhang, X. / Chen, Z.

Citation

Journal: Structure / Year: 2012
Title: Complex Structures of the Abscisic Acid Receptor PYL3/RCAR13 Reveal a Unique Regulatory Mechanism
Authors: Zhang, X. / Zhang, Q. / Xin, Q. / Yu, L. / Wang, Z. / Wu, W. / Jiang, L. / Wang, G. / Tian, W. / Deng, Z. / Wang, Y. / Liu, Z. / Long, J. / Gong, Z. / Chen, Z.

History

Deposition	Feb 18, 2012	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 6, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / 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: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_label_asym_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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PDBx/mmCIF format	4dsc.cif.gz	179.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4dsc.ent.gz	143.7 KB	Display	PDB format
PDBx/mmJSON format	4dsc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4dsc_validation.pdf.gz	1015.3 KB	Display	wwPDB validaton report
Full document	4dsc_full_validation.pdf.gz	1021.1 KB	Display
Data in XML	4dsc_validation.xml.gz	22.7 KB	Display
Data in CIF	4dsc_validation.cif.gz	34.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ds/4dsc ftp://data.pdbj.org/pub/pdb/validation_reports/ds/4dsc	HTTPS FTP

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Related structure data

Related structure data	3kl1C 3klxSC 3ojiC 4ds8C 4dsbC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4jda-2 4jda-1 4dsb-d 6mjw-d 3mr7-2 6c3i-1 1wkf-d 3hfj-d 3faa-4 6vhx-1 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

Deposited unit

A: Abscisic acid receptor PYL3

B: Abscisic acid receptor PYL3

hetero molecules

43 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)	232.836, 232.836, 53.292
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	B-485- HOH

#1: Protein	Abscisic acid receptor PYL3 / PYR1-like protein 3 / Regulatory components of ABA receptor 13 Mass: 21227.234 Da / Num. of mol.: 2 / Fragment: UNP residues 25-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g73000, PYL3 / Plasmid: pgex 4t-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) cells / References: UniProt: Q9SSM7
#2: Chemical	ChemComp-A8S / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid / (+)-abscisic acid / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexen-1-yl]-3-methyl-2,4-pentadienoic acid Mass: 264.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₀O₄
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 607 / 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: 3.27 Å³/Da / Density % sol: 62.43 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 1.6M (NH)2SO4, 0.1M HEPES, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 29, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. all: 40074 / Num. obs: 39972 / % possible obs: 99.75 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.8 % / R_merge(I) obs: 0.096
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.469 / Num. unique all: 1981 / % possible all: 4.9

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.6.0117	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KLX

3klx

Resolution: 1.95→38.81 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.482 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21071	1997	5 %	RANDOM
R_work	0.18484	37938	-	-
obs	0.18616	37938	99.75 %	-

Solvent computation

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

Displacement parameters

B_iso max: 90.81 Å² / B_iso mean: 31.8795 Å² / B_iso min: 11.09 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.74 Å²	0.37 Å²	-0 Å²
2-	-	0.74 Å²	-0 Å²
3-	-	-	-1.11 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→38.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2653	0	40	607	3300

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.02	2767
X-RAY DIFFRACTION	r_angle_refined_deg	1.323	1.955	3783
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.209	5	355
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.696	23.364	107
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.621	15	427
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.117	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.261	0.2	465
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	2060
X-RAY DIFFRACTION	r_rigid_bond_restr	3.435	3	2767
X-RAY DIFFRACTION	r_sphericity_free	25.248	5	117
X-RAY DIFFRACTION	r_sphericity_bonded	14.228	5	3208

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.28	139	-
R_work	0.22	2707	-
all	-	2846	-
obs	-	-	99.48 %

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	4.44	1.4083	-0.3452	2.8782	-0.2728	0.1559	-0.071	-0.0429	-0.3024	0.0421	0.068	-0.285	0.1784	0.0066	0.003	0.2709	0.0347	-0.043	0.1784	0.0183	0.1457	47.8795	-42.3219	27.146
2	0.6432	0.4024	-0.0569	1.5875	0.3945	0.6669	0.0105	-0.0041	-0.0076	-0.0564	0.0369	-0.0582	0.0019	0.0309	-0.0474	0.1685	0.0086	-0.0087	0.1644	0.0139	0.1502	44.3166	-32.0812	23.4816
3	0.4854	-0.0643	-0.6923	0.7204	-0.1017	1.0475	0.011	0.0458	0.0226	0.015	0.0145	0.0853	-0.0256	-0.0825	-0.0255	0.1505	-0.004	0.0023	0.1601	0.002	0.1599	31.3923	-24.6164	21.824
4	4.65	2.3069	1.39	1.1446	0.6957	1.0801	-0.0943	-0.0184	0.2955	-0.0496	-0.009	0.1499	-0.2198	-0.0379	0.1033	0.2008	-0.0017	-0.0069	0.1706	-0.0181	0.1951	25.5399	-28.6997	33.6521
5	1.0917	0.2945	0.0516	0.6139	-0.1317	1.3763	0.0014	0.0791	-0.0131	-0.0572	0.033	0.0509	0.0952	-0.1477	-0.0344	0.1622	-0.0024	0.0027	0.1684	-0.0044	0.1617	26.3249	-31.0312	18.0641
6	0.8828	0.5144	1.0013	0.352	0.5221	1.7672	-0.0056	-0.0712	-0.0408	0.064	0.0021	-0.006	0.0382	-0.0506	0.0035	0.175	-0.0006	0.0047	0.1808	0.0015	0.1716	35.0929	-34.5721	30.1503
7	3.5924	3.1093	-8.4935	2.6932	-7.3511	20.0935	-0.8962	0.2071	-0.5768	-0.4916	-0.1297	-0.5024	1.3966	-0.5459	1.0259	0.5438	-0.0934	0.1357	0.5256	-0.0647	0.5696	27.0981	-39.9128	14.1347
8	0.5695	-0.3139	0.0945	0.2051	0.0648	0.4451	0.0474	0.028	0.0241	-0.0048	0.0051	-0.0298	0.105	0.0876	-0.0524	0.1723	-0.0009	0.0061	0.1887	0.0064	0.1722	47.1239	-31.787	27.5018
9	1.1056	0.5435	0.5796	1.0965	0.6459	0.7223	0.0332	0.0102	-0.1013	0.0225	0.0106	-0.0778	0.0934	0.0581	-0.0438	0.1651	-0.0084	-0.0031	0.1634	-0.0054	0.1609	44.548	-35.1679	22.0184
10	3.5428	2.4382	3.7742	10.1672	7.3929	7.4106	-0.3717	0.4016	-0.0766	-1.0221	0.512	0.2428	-0.3669	0.2802	-0.1402	0.5317	-0.2961	-0.1666	0.3136	0.0297	0.115	37.4986	-43.7781	7.5285
11	0.1222	-0.6294	-0.1839	3.4577	0.4643	1.6998	0.0083	-0.0013	0.0008	-0.0608	0.0203	-0.0785	0.0743	0.0186	-0.0286	0.1361	-0.0027	0.0026	0.1528	0.0041	0.1428	42.2692	-28.7854	15.8505
12	10.1506	6.8371	2.2326	5.9925	3.5434	3.4952	-0.1941	0.4437	1.1718	-0.4691	0.5632	0.3658	-0.5414	0.4498	-0.369	0.3154	-0.0371	0.0199	0.2018	0.0115	0.3381	47.9589	-14.7576	22.8547
13	0.7554	-1.1138	-0.0671	2.8138	-0.3271	0.5172	0.021	0.003	0.0608	0.0247	-0.0361	-0.1187	0.0025	0.0284	0.015	0.1639	-0.0031	0.0009	0.1799	0.0084	0.1678	59.6928	-22.9603	-1.8351
14	0.7933	0.4233	0.2689	1.3504	-0.1434	0.6056	0.0772	-0.0558	-0.0461	0.0461	-0.0368	-0.077	0.0579	-0.0258	-0.0404	0.1463	0.0091	0.0208	0.17	-0.0069	0.1442	49.7039	-22.1014	2.1494
15	0.6013	-0.5638	-0.1763	0.9151	-0.521	1.5463	0.0009	0.0145	0.047	0.0105	0.0019	0.0514	-0.0402	-0.1132	-0.0029	0.1407	-0.0096	-0.0015	0.1508	-0.0034	0.1628	36.8903	-15.8862	4.3813
16	0.5621	-0.1808	-0.1067	0.9623	0.2296	0.9002	0.0092	0.0105	0.0229	-0.0444	0.0036	-0.0304	-0.0599	0.0043	-0.0128	0.1553	-0.0036	-0.0019	0.1508	0.0092	0.1583	41.9025	-9.7896	0.5847
17	4.6333	-1.8956	-2.0572	1.9251	0.1586	1.3207	-0.0144	-0.3076	0.3273	0.1132	0.1006	-0.243	-0.0622	0.1665	-0.0862	0.1962	-0.0122	-0.0266	0.2108	-0.0304	0.1909	48.7173	-5.2547	10.252
18	0.7227	-0.0019	-0.0745	0.6341	-0.1996	0.3601	-0.0241	0.0051	-0.0352	-0.073	-0.008	-0.1055	0.0766	0.0727	0.0321	0.1491	-0.0001	-0.0031	0.1611	-0.0015	0.159	51.7938	-24.2253	0.6644
19	3.15	4.5473	0.8827	6.7088	0.7609	4.1415	0.1774	-0.2933	-0.0171	0.3107	-0.2977	-0.0432	-0.0522	0.0444	0.1203	0.1911	0.0244	-0.0168	0.2993	-0.0164	0.1561	56.6234	-11.7834	17.6437
20	2.5316	1.818	0.9498	3.4016	1.1118	2.4282	0.0293	-0.0108	-0.1025	-0.0078	0.0057	-0.0432	0.0924	-0.0476	-0.035	0.1406	0.012	0.0093	0.1326	0.0062	0.1354	43.3862	-25.5034	7.931

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	26 - 46
2	X-RAY DIFFRACTION	2	A	47 - 67
3	X-RAY DIFFRACTION	3	A	68 - 88
4	X-RAY DIFFRACTION	4	A	89 - 99
5	X-RAY DIFFRACTION	5	A	100 - 120
6	X-RAY DIFFRACTION	6	A	121 - 137
7	X-RAY DIFFRACTION	7	A	138 - 143
8	X-RAY DIFFRACTION	8	A	144 - 162
9	X-RAY DIFFRACTION	9	A	163 - 176
10	X-RAY DIFFRACTION	10	A	177 - 188
11	X-RAY DIFFRACTION	11	A	189 - 202
12	X-RAY DIFFRACTION	12	A	203 - 209
13	X-RAY DIFFRACTION	13	B	22 - 45
14	X-RAY DIFFRACTION	14	B	46 - 67
15	X-RAY DIFFRACTION	15	B	68 - 87
16	X-RAY DIFFRACTION	16	B	88 - 135
17	X-RAY DIFFRACTION	17	B	136 - 145
18	X-RAY DIFFRACTION	18	B	146 - 176
19	X-RAY DIFFRACTION	19	B	177 - 189
20	X-RAY DIFFRACTION	20	B	190 - 207

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