PDB-4dsb: Complex Structure of Abscisic Acid Receptor PYL3 with (+)-ABA in ...

ID or keywords:

Entry

Database: PDB / ID: 4dsb

Title

Complex Structure of Abscisic Acid Receptor PYL3 with (+)-ABA in Spacegroup of I 212121 at 2.70A

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 /

MIR / Resolution: 2.7 Å

Authors

Zhang, X. / Zhang, Q. / 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 / struct_site Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	4dsb.cif.gz	153 KB	Display	PDBx/mmCIF format
PDB format	pdb4dsb.ent.gz	120.9 KB	Display	PDB format
PDBx/mmJSON format	4dsb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4dsb_validation.pdf.gz	982.6 KB	Display	wwPDB validaton report
Full document	4dsb_full_validation.pdf.gz	990.2 KB	Display
Data in XML	4dsb_validation.xml.gz	17.2 KB	Display
Data in CIF	4dsb_validation.cif.gz	23.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ds/4dsb ftp://data.pdbj.org/pub/pdb/validation_reports/ds/4dsb	HTTPS FTP

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Related structure data

Related structure data	3kl1C 3klxSC 3ojiC 4ds8C 4dscC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5jgm-d 6lyj-2 2oah-d 4giy-d 1q2r-2 1jqp-d 4jda-2 2vn8-2 4lkv-3 3ckp-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

42.4 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)	63.189, 89.041, 206.685
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	24
Space group name H-M	I2₁2₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	B-435- HOH

#1: Protein	Abscisic acid receptor PYL3 / PYR1-like protein 3 / Regulatory components of ABA receptor 13 Mass: 20957.891 Da / Num. of mol.: 2 / Fragment: UNP residues 24-209 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.47 Å³/Da / Density % sol: 64.53 %
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: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. all: 18008 / Num. obs: 16637 / % possible obs: 92.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.9 % / R_merge(I) obs: 0.077
Reflection shell	Resolution: 2.7→2.75 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.591 / Num. unique all: 724 / % possible all: 4

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Processing

Software

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

Refinement

Method to determine structure:

MIR
Starting model: 3KLX

3klx

Resolution: 2.7→50 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.907 / Occupancy max: 1 / Occupancy min: 0.04 / SU B: 32.844 / SU ML: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.35 / 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	0.2903	762	5 %	RANDOM
R_work	0.2076	14552	-	-
obs	0.2119	15314	92.77 %	-

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 max: 218.48 Å² / B_iso mean: 80.0378 Å² / B_iso min: 51.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	0 Å²	0 Å²
2-	-	9.11 Å²	0 Å²
3-	-	-	-9.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2509	0	38	122	2669

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.02	2593
X-RAY DIFFRACTION	r_angle_refined_deg	1.786	1.945	3555
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.427	5	345
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.853	23.656	93
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.877	15	340
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.084	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.169	0.2	439
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	1962
X-RAY DIFFRACTION	r_rigid_bond_restr	3.46	3	2593
X-RAY DIFFRACTION	r_sphericity_free	38.708	5	115
X-RAY DIFFRACTION	r_sphericity_bonded	22.814	5	2554

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.528	40	-
R_work	0.237	934	-
all	-	974	-
obs	-	-	87.35 %

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	4.9459	1.0701	3.4758	3.0601	-0.625	3.1154	0.1657	0.1257	-0.0945	0.0041	0.0862	0.3805	0.1488	0.074	-0.2519	0.2463	0.0228	0.0992	0.1961	-0.0223	0.212	-9.1507	6.7211	39.1086
2	1.9075	0.8658	1.0544	1.4148	-0.2042	2.0585	-0.0654	0.3197	-0.3144	-0.032	0.1206	-0.015	0.4177	-0.0182	-0.0553	0.3087	-0.0184	0.1102	0.176	-0.0696	0.1503	4.1107	-4.741	30.0118
3	3.574	0.1011	0.5177	1.3984	-0.4068	3.3818	-0.0634	-0.144	0.0043	0.261	-0.1318	-0.0085	0.0927	-0.1568	0.1953	0.2455	-0.0016	0.0364	0.0388	0.0207	0.1144	4.1373	-3.9008	38.476
4	13.3869	4.456	15.2678	4.959	6.9465	18.4237	0.1824	0.4065	-0.2317	0.3163	0.1473	-0.1515	0.3302	0.4231	-0.3297	0.1308	-0.0176	0.0754	0.2699	0.0728	0.1083	0.07	5.8879	37.3043
5	1.2512	-1.4299	-6.2355	20.9477	15.4717	34.7214	0.2083	-0.0507	-0.0504	0.603	-0.452	-0.162	-0.7606	0.0989	0.2437	0.3902	-0.0505	-0.097	0.1306	0.1694	0.2393	7.4829	14.261	41.8862
6	0.2143	-1.2043	0.4904	7.7468	-0.6037	10.3325	-0.0992	0.0824	-0.1296	0.219	-0.2214	0.9581	-0.1765	0.304	0.3206	0.1918	-0.1592	0.0103	0.1477	0.004	0.1427	4.5923	3.3587	26.4948
7	3.2895	1.7053	-0.7035	6.0434	2.9828	3.0164	-0.1094	-0.167	0.545	-0.4112	-0.0163	0.3587	-0.6569	0.0932	0.1257	0.3567	0.061	-0.106	0.2309	0.0891	0.205	9.2776	23.8466	10.9014
8	2.4596	-1.6862	-2.9792	3.2277	0.6179	5.0711	0.0928	0.1672	0.178	0.1288	0.0086	-0.0009	-0.5046	-0.8154	-0.1014	0.192	0.2299	-0.1529	0.6436	-0.1261	0.2084	10.9183	17.5597	21.6936
9	0.4298	0.2595	-1.0521	0.1592	-0.6342	2.5852	-0.0321	-0.1839	-0.066	-0.0229	-0.1113	-0.0632	0.1016	0.4855	0.1434	0.1546	0.0855	-0.0111	0.2185	0.0034	0.2414	23.0432	11.0228	21.9237
10	4.9493	3.4534	-4.8554	7.14	-0.5027	6.523	-0.1377	0.0052	-0.135	-0.1114	-0.1388	0.1468	0.1219	-0.0893	0.2765	0.2075	0.1299	-0.0125	0.1819	0.0628	0.0837	18.9083	2.0222	20.0481
11	21.4728	-10.6073	10.423	5.2421	-5.1491	5.0611	-0.0626	-0.9249	-0.9637	0.0282	0.4943	0.4328	-0.054	-0.4104	-0.4317	0.6485	-0.2915	0.1079	1.0786	-0.1075	0.9522	36.2268	4.4775	10.4605
12	17.5871	20.0491	13.2117	23.2314	15.4353	10.3104	3.3612	-0.9301	-0.9858	4.2167	-1.4875	-1.897	2.771	-0.694	-1.8738	0.7838	-0.216	-0.1788	0.6031	0.1203	1.6633	25.0685	5.6651	12.7126
13	3.5961	-1.3903	0.4296	0.5565	0.025	1.9909	-0.0935	0.1863	-0.3231	0.07	-0.0516	0.1429	0.3854	0.2899	0.1451	0.1979	0.0798	0.054	0.133	0.0281	0.0513	18.5116	4.4803	12.3209
14	1.7677	0.8748	0.1709	11.591	5.7586	10.5317	-0.1777	0.6542	0.2492	0.0549	0.4151	-0.0009	-0.2104	1.0655	-0.2374	0.0293	-0.0973	-0.0172	0.3627	0.0679	0.0548	20.5658	13.3427	12.3642
15	4.738	1.8203	-4.2761	14.0736	-1.994	3.8707	-0.7618	0.6574	0.0421	-0.0787	0.7971	0.3557	0.7007	-0.5914	-0.0353	0.314	-0.0319	0.0303	0.2339	0.0422	0.2304	12.21	3.9732	6.2111
16	4.4485	-1.3498	-0.4997	9.8211	2.2059	0.5134	0.1215	0.1918	0.2633	0.6393	-0.1996	0.2171	0.0848	-0.0883	0.0781	0.3305	0.1706	-0.1837	0.2098	-0.0588	0.2386	13.8389	22.6257	23.7714
17	4.9989	4.7907	8.4722	5.4884	7.079	15.5719	0.3368	-0.2782	-0.0665	0.2374	-0.2801	-0.1184	0.7179	-0.4757	-0.0567	0.1021	-0.059	0.0297	0.0522	-0.0346	0.0523	9.8726	14.2453	12.5959
18	22.972	-14.6117	-25.8823	20.3175	23.4425	33.5811	-0.3156	0.3515	-0.4627	0.8716	-0.3076	0.4166	0.7932	-0.4599	0.6232	0.1681	-0.0471	-0.0201	0.0979	-0.0328	0.2542	0.3938	4.1103	4.483
19	26.2114	-13.1681	5.3847	18.1004	-2.5015	19.8384	0.3562	0.2741	-0.0625	0.7508	-0.7449	0.1562	0.2347	-0.6847	0.3888	0.1025	-0.0411	-0.0027	0.2096	0.0022	0.028	2.6982	7.0624	11.7638
20	3.2562	-0.1518	3.1574	5.1426	0.4331	3.1392	-0.027	-0.2204	0.5613	0.785	-0.5631	0.0719	0.0329	-0.2849	0.5901	0.159	-0.0649	-0.0236	0.1214	-0.0257	0.1846	11.1939	9.867	24.8741

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	24 - 52
2	X-RAY DIFFRACTION	2	A	53 - 90
3	X-RAY DIFFRACTION	3	A	95 - 155
4	X-RAY DIFFRACTION	4	A	164 - 179
5	X-RAY DIFFRACTION	5	A	180 - 189
6	X-RAY DIFFRACTION	6	A	190 - 206
7	X-RAY DIFFRACTION	7	B	27 - 48
8	X-RAY DIFFRACTION	8	B	49 - 64
9	X-RAY DIFFRACTION	9	B	65 - 76
10	X-RAY DIFFRACTION	10	B	77 - 87
11	X-RAY DIFFRACTION	11	B	88 - 96
12	X-RAY DIFFRACTION	12	B	97 - 107
13	X-RAY DIFFRACTION	13	B	108 - 124
14	X-RAY DIFFRACTION	14	B	125 - 138
15	X-RAY DIFFRACTION	15	B	139 - 144
16	X-RAY DIFFRACTION	16	B	145 - 165
17	X-RAY DIFFRACTION	17	B	166 - 176
18	X-RAY DIFFRACTION	18	B	177 - 184
19	X-RAY DIFFRACTION	19	B	185 - 189
20	X-RAY DIFFRACTION	20	B	190 - 206

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