PDB-4jda: Complex structure of abscisic acid receptor PYL3 with (-)-ABA

ID or keywords:

Entry

Database: PDB / ID: 4jda

Title

Complex structure of abscisic acid receptor PYL3 with (-)-ABA

Components

Abscisic acid receptor PYL3

Keywords

HORMONE RECEPTOR / abscisic acid receptor / PP2C

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: 2.65 Å

Authors

Zhang, X. / Wang, G. / Chen, Z.

Citation

Journal: Plos One / Year: 2013
Title: Structural Insights into the Abscisic Acid Stereospecificity by the ABA Receptors PYR/PYL/RCAR
Authors: Zhang, X. / Jiang, L. / Wang, G. / Yu, L. / Zhang, Q. / Xin, Q. / Wu, W. / Gong, Z. / Chen, Z.

History

Deposition	Feb 24, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 24, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 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 / 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 / _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

-
Download

PDBx/mmCIF format	4jda.cif.gz	276.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4jda.ent.gz	226.4 KB	Display	PDB format
PDBx/mmJSON format	4jda.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4jda_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	4jda_full_validation.pdf.gz	1.3 MB	Display
Data in XML	4jda_validation.xml.gz	27.8 KB	Display
Data in CIF	4jda_validation.cif.gz	37.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jd/4jda ftp://data.pdbj.org/pub/pdb/validation_reports/jd/4jda	HTTPS FTP

-
Related structure data

Related structure data	3oquC 4jdlC 4dscS 3kl1 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6fs8-d 6rp7-d 2oah-d 1xc8-d 4dsc-d 1cmk-d 4ae9-1 6m1x-1 3isq-d 6osp-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Abscisic acid receptor PYL3

B: Abscisic acid receptor PYL3

C: Abscisic acid receptor PYL3

D: Abscisic acid receptor PYL3

hetero molecules

87.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Abscisic acid receptor PYL3

B: Abscisic acid receptor PYL3

hetero molecules

defined by author&software
43.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Abscisic acid receptor PYL3

D: Abscisic acid receptor PYL3

hetero molecules

defined by author&software
43.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	142.738, 142.738, 99.802
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Abscisic acid receptor PYL3 / PYR1-like protein 3 / Regulatory components of ABA receptor 13 Mass: 21645.680 Da / Num. of mol.: 4 / Fragment: UNP residues 21-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL3 / Plasmid: pgex 4t-2 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Rosetta 2 (DE3) cells / References: UniProt: Q9SSM7
#2: Chemical	ChemComp-A9S / (2Z,4E)-5-[(1R)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid Mass: 264.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₀O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.39 Å³/Da / Density % sol: 63.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 8000, 0.1M Tris-HCl, 0.2M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 130 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 1, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.65→50 Å / Num. all: 33679 / Num. obs: 32032 / % possible obs: 95.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shell	Resolution: 2.65→2.7 Å / Num. unique all: 1198 / % possible all: 70.8

-
Processing

Software

Name	Version	Classification
MAR345dtb		data collection
PHASER		phasing
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4DSC

4dsc

Resolution: 2.65→38.12 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.918 / SU B: 26.481 / SU ML: 0.263 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.564 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26728	1544	5 %	RANDOM
R_work	0.24332	-	-	-
all	0.24459	33679	-	-
obs	0.24459	29323	91.68 %	-

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: 63.446 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.67 Å²	-3.67 Å²	-0 Å²
2-	-	-3.67 Å²	-0 Å²
3-	-	-	11.9 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→38.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5225	0	76	95	5396

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	5396
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4957
X-RAY DIFFRACTION	r_angle_refined_deg	1.287	1.951	7372
X-RAY DIFFRACTION	r_angle_other_deg	0.769	3	11260
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.866	5	683
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.325	23.163	215
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.622	15	790
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.663	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	901
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	6121
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1269

LS refinement shell

Resolution: 2.651→2.719 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.485	81	-
R_work	0.347	1559	-
obs	-	-	66.05 %

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	1.4149	-0.1911	0.491	1.339	0.3078	0.402	0.0182	0.0467	-0.0337	-0.0797	0.1451	-0.0766	-0.0283	0.0004	-0.1633	0.1949	-0.0287	0.0133	0.3246	0.0251	0.121	48.3626	-68.3526	5.8849
2	1.2837	0.8336	1.6545	2.5461	3.0297	8.7366	0.0421	0.0087	-0.2934	0.1709	0.0025	-0.1296	0.4747	-0.0023	-0.0445	0.2102	-0.0709	-0.0573	0.2079	0.0087	0.1119	47.9327	-86.515	11.9757
3	1.9489	-0.2072	-0.3861	0.7756	0.0156	0.5018	0.0994	0.1279	-0.0538	0.0415	0.0822	-0.0325	-0.0255	-0.1358	-0.1816	0.1894	-0.0644	-0.0214	0.3233	0.0383	0.0901	45.6242	-71.5666	7.9061
4	10.37	-0.334	-4.2436	0.1573	0.0681	3.0088	0.0297	-0.336	0.2671	-0.0944	-0.0451	-0.0173	-0.3276	0.304	0.0154	0.2366	-0.0346	-0.0315	0.3423	0.0189	0.0195	54.6691	-69.8636	13.5874
5	17.4979	5.6862	2.7678	7.6144	-0.3753	0.7247	0.2618	0.0998	1.1091	0.3421	-0.517	-0.0078	-0.0631	0.1456	0.2552	0.4721	-0.0215	0.0336	0.2934	0.0103	0.1004	67.0914	-52.3942	27.7079
6	3.7158	1.1201	-1.2048	0.9834	-0.0021	2.687	0.1958	-0.2892	0.4151	0.0313	-0.0463	0.2345	-0.0689	0.2966	-0.1495	0.1756	-0.0792	-0.04	0.3053	0.0156	0.09	67.3345	-62.7156	24.84
7	1.9406	-0.7636	-0.0253	0.3044	-0.0057	0.1731	-0.0555	0.0521	-0.1829	0.0334	-0.0503	0.0563	0.0689	0.1115	0.1058	0.2313	-0.0027	-0.0223	0.4114	0.0967	0.098	72.0754	-77.2275	24.8117
8	1.5297	-0.2903	-0.5096	0.7353	-0.1643	1.3721	0.0149	0.1414	0.1119	0.1377	0.0006	-0.0232	0.0032	0.0865	-0.0155	0.1992	-0.0657	-0.0521	0.3719	0.0405	0.026	68.9894	-65.6585	20.6263
9	6.2316	-0.9241	-0.7578	1.8836	0.1495	0.0995	-0.0199	-0.1054	-0.5821	-0.1557	-0.0668	0.1575	-0.0064	0.0631	0.0867	0.1762	-0.0358	-0.0373	0.4244	0.0446	0.0663	27.77	-64.6612	3.6934
10	2.7088	-0.9908	1.9889	1.6738	-0.2844	1.6178	0.0392	0.203	-0.1691	0.0422	0.0685	0.1308	0.0151	0.1869	-0.1078	0.1645	-0.0365	0.0207	0.3731	0.039	0.0243	19.7031	-54.2079	4.2176
11	1.166	-0.7153	0.3694	1.721	0.4684	2.9455	-0.0347	0.0881	0.1858	0.0654	0.0219	0.0166	-0.222	0.0922	0.0129	0.1785	-0.102	0.0246	0.2625	0.047	0.0566	23.0474	-42.4806	7.3118
12	1.8541	-0.0882	1.0274	1.0255	0.3286	1.7943	0.084	-0.1018	-0.1046	0.0982	0.0397	0.0488	0.0878	-0.0727	-0.1237	0.1548	-0.0411	-0.0007	0.311	0.0586	0.0222	20.3814	-56.3778	9.3394
13	3.4229	-11.3136	-2.2863	37.4053	7.558	1.5275	-0.0664	-0.0087	-0.1352	0.1987	-0.013	0.4187	0.047	-0.003	0.0794	0.1565	-0.065	-0.1214	0.2823	0.2695	0.2977	8.8302	-72.6055	25.8964
14	2.6408	-1.2315	-1.5647	0.5932	0.7164	0.9372	-0.0887	-0.1202	-0.0374	-0.0518	0.1079	0.052	0.1035	0.0119	-0.0192	0.4087	-0.2542	-0.1462	0.4827	0.1886	0.0818	-5.0019	-67.1482	26.0148
15	2.0192	0.2982	0.2377	0.2657	0.1294	0.4467	0.054	-0.2137	0.2963	0.0589	-0.0943	-0.0402	0.166	-0.1518	0.0404	0.1845	-0.0226	0.0266	0.3316	-0.0029	0.0845	3.1503	-50.4264	23.42
16	2.4723	0.7528	-0.4484	0.3585	-0.8925	4.5023	0.2505	-0.2134	0.4451	0.0235	-0.0664	0.153	0.2514	0.0525	-0.1841	0.2057	0.035	0.0655	0.3539	-0.0132	0.0881	-4.927	-49.1654	22.9174
17	2.5608	-0.1646	0.608	0.7634	0.4118	1.8527	0.1292	-0.0953	0.0061	0.0701	-0.0726	0.1313	0.2328	-0.1454	-0.0566	0.1676	-0.0415	0.0361	0.3586	0.0303	0.0511	-0.6069	-59.0028	20.4934
18	6.1966	3.853	4.0694	2.533	3.081	4.9361	0.0319	0.0909	-0.4937	-0.0085	0.0626	-0.2562	0.0093	-0.0175	-0.0945	0.1803	-0.0692	0.0387	0.3668	0.0174	0.0781	5.8718	-57.3834	15.3796

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	23 - 81
2	X-RAY DIFFRACTION	2	A	82 - 120
3	X-RAY DIFFRACTION	3	A	121 - 185
4	X-RAY DIFFRACTION	4	A	186 - 207
5	X-RAY DIFFRACTION	5	B	23 - 42
6	X-RAY DIFFRACTION	6	B	43 - 67
7	X-RAY DIFFRACTION	7	B	68 - 126
8	X-RAY DIFFRACTION	8	B	127 - 206
9	X-RAY DIFFRACTION	9	C	23 - 45
10	X-RAY DIFFRACTION	10	C	46 - 73
11	X-RAY DIFFRACTION	11	C	74 - 144
12	X-RAY DIFFRACTION	12	C	145 - 207
13	X-RAY DIFFRACTION	13	D	23 - 30
14	X-RAY DIFFRACTION	14	D	31 - 48
15	X-RAY DIFFRACTION	15	D	49 - 91
16	X-RAY DIFFRACTION	16	D	96 - 135
17	X-RAY DIFFRACTION	17	D	136 - 180
18	X-RAY DIFFRACTION	18	D	181 - 207

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi