PDB-3klx: Crystal structure of native abscisic acid receptor PYL3

ID or keywords:

Entry

Database: PDB / ID: 3klx

Title

Crystal structure of native abscisic acid receptor PYL3

Components

F3N23.20 protein

Keywords

HORMONE RECEPTOR / abscisic acid receptor / crystal / 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 /

SAD / Resolution: 2.5 Å

Authors

Zhang, X. / Wang, G. / 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	Nov 9, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 10, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jun 6, 2012	Group: Database references
Revision 1.3	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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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PDBx/mmCIF format	3klx.cif.gz	152.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3klx.ent.gz	123.8 KB	Display	PDB format
PDBx/mmJSON format	3klx.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3klx_validation.pdf.gz	445.9 KB	Display	wwPDB validaton report
Full document	3klx_full_validation.pdf.gz	453.9 KB	Display
Data in XML	3klx_validation.xml.gz	16.6 KB	Display
Data in CIF	3klx_validation.cif.gz	22.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kl/3klx ftp://data.pdbj.org/pub/pdb/validation_reports/kl/3klx	HTTPS FTP

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Related structure data

Related structure data	3kl1C 3ojiC 4ds8C 4dsbC 4dscC C: citing same article (ref.)
Similar structure data	1w30-d 6zj4-d 6s2t-d 5wmk-d 3jsa-d 7aab-2 5u7b-d 3b0b-d 4iyr-d 3kl1-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

Deposited unit

A: F3N23.20 protein

B: F3N23.20 protein

hetero molecules

46.8 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)	86.964, 86.964, 154.118
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	F3N23.20 protein / PYL3 Mass: 23323.404 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g73000, F3N23.20, pyl3 / Plasmid: pgex 4t-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q9SSM7
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 3.12 Å³/Da / Density % sol: 60.62 %
Crystal grow	Temperature: 298 K / Method: evaporation / pH: 8 Details: 20mM tris, 2.0M ammonium sulfate, pH 8, EVAPORATION, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	130	1
2	130	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	Photon Factory	AR-NE3A	1	1
SYNCHROTRON	Photon Factory	AR-NW12A	2	1

Detector

Type	ID	Detector	Date
ADSC QUANTUM 270	1	CCD	Oct 25, 2009
ADSC QUANTUM 270	2	CCD	Oct 25, 2009

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SAD	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.5→20 Å / Num. all: 21065 / Num. obs: 19933 / % possible obs: 95.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / R_sym value: 0.055

Reflection shell

Resolution: 2.5→2.56 Å / % possible all: 7.2

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
SHARP		phasing
REFMAC	5.5.0072	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.5→20 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.929 / SU B: 20.802 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26959	1049	5 %	RANDOM
R_work	0.25206	-	-	-
obs	0.25298	19933	99.37 %	-
all	-	21065	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 71.891 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.36 Å²	0 Å²	0 Å²
2-	-	-0.36 Å²	0 Å²
3-	-	-	0.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2749	0	10	124	2883

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	2805
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.147	1.946	3825
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.381	5	354
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.11	23.304	115
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.672	15	435
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.15	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	472
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	2072
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.627	1.5	1800
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.144	2	2930
X-RAY DIFFRACTION	r_scbond_it	1.045	3	1005
X-RAY DIFFRACTION	r_scangle_it	1.804	4.5	895
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.5→2.564 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.675	84	-
R_work	0.596	1442	-
obs	-	-	100 %

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	3.6862	1.1715	-0.3418	10.4646	-2.4401	2.8579	0.0476	-0.8088	-0.2923	1.5238	-0.0459	0.2025	-0.3637	0.4033	-0.0016	0.616	0.1664	0.0093	0.604	0.1732	0.3981	80.503	42.672	76.728
2	3.4202	-0.9896	-0.476	8.2148	-1.0968	4.3273	-0.1084	0.0135	-0.003	0.1135	0.0781	0.1219	0.5938	0.2816	0.0304	0.1542	0.1255	-0.0101	0.4443	0.176	0.3558	80.898	44.275	64.814
3	4.145	2.1143	3.9868	1.4286	0.5534	13.3903	-0.0862	0.5075	-0.0546	-0.3274	0.0186	-0.2174	1.0868	0.5082	0.0676	0.4593	0.1221	0.1275	0.7456	0.0843	0.5414	88.177	49.63	54.438
4	1.4542	-0.6183	0.2219	4.444	-1.0138	0.2393	0.0571	0.2517	0.2882	-0.328	-0.01	0.2519	0.0655	0.0593	-0.0472	0.1023	-0.0953	0.0697	0.6471	0.0614	0.3085	85.855	56.026	53.702
5	5.7746	0.0416	1.1914	5.0964	0.2807	2.3607	-0.1107	0.0218	0.4019	-0.1386	0.0815	-0.346	-0.0612	0.8945	0.0292	0.066	-0.0248	0.0621	0.6571	0.1124	0.4107	87.995	55.371	60.494
6	2.7106	2.4016	-0.8858	5.4695	-0.6245	2.8773	0.1802	-0.0927	0.264	0.3326	0.0626	-0.2229	-0.2124	0.6199	-0.2427	0.1704	0.0171	0.041	0.5687	0.1613	0.4333	83.404	52.581	66.203
7	7.7173	5.6487	3.322	16.6926	9.8502	9.8058	-0.3014	0.5504	-0.76	-0.6189	0.6274	-0.621	0.5483	-0.0224	-0.326	1.0099	0.0879	-0.1095	0.6514	0.0858	0.5866	78.86	22.64	65.355
8	1.5944	2.1564	-0.2089	3.3907	0.0751	3.7563	0.0835	-0.0668	0.4717	0.0874	0.2891	0.4129	-0.1522	0.3222	-0.3726	0.2554	0.0862	0.122	0.5736	0.1289	0.65	74.65	56.217	70.131
9	3.5928	-3.6298	-2.1654	7.5703	4.0075	6.1903	-0.0357	0.3272	-0.1349	-0.2264	0.1836	0.8279	0.3729	-0.3341	-0.1479	0.3286	0.0477	-0.0129	0.635	0.2149	0.647	74.628	47.411	59.838
10	1.1584	1.2755	-1.742	9.7133	-7.5774	16.1072	-0.6521	0.1119	-0.0643	0.0265	0.6461	0.054	0.4413	-0.599	0.006	0.6557	-0.3228	0.1168	0.6607	0.0416	0.7863	69.607	45.024	35.065
11	17.0097	0.7995	3.5269	5.5723	8.7523	14.1801	-0.5435	0.869	-0.5276	-1.4467	-0.0178	0.4878	-2.076	-0.2912	0.5614	1.1229	-0.7893	-0.1202	1.129	0.2527	0.4546	59.383	45.048	35.417
12	5.1602	0.9641	-3.7776	6.3637	-0.3957	5.2278	-0.5969	0.6293	0.005	-0.4123	0.6367	0.453	1.0549	-1.3173	-0.0398	0.248	-0.3162	-0.0213	0.5582	0.2846	0.4579	58.649	46.159	49.039
13	5.3211	-3.6101	0.1201	2.5815	0.5138	3.9501	-0.0035	-0.0786	-0.0078	0.083	0.1073	0.0948	0.1589	-0.3471	-0.1037	0.0947	0.0271	0.1026	0.3733	0.2658	0.4178	55.837	53.819	60.56
14	7.6706	-4.7472	1.7406	3.3509	-2.3798	4.5044	-0.1074	0.19	0.0576	0.1187	0.1508	-0.0111	-0.1713	-0.7625	-0.0434	0.0318	0.0493	0.0947	0.4797	0.2193	0.3962	51.999	57.146	57.497
15	3.15	0.6449	-0.1765	9.9343	3.3662	5.1862	0.0742	0.2479	-0.1514	-0.1153	0.5045	-0.0208	0.0036	-1.46	-0.5787	0.0342	-0.0109	0.0479	0.8558	0.3639	0.6536	52.917	54.106	50.658
16	3.6033	-1.2904	-3.8767	7.7938	2.7431	4.479	0.5701	0.2207	0.3125	-0.2372	-0.1913	-0.0941	-0.5944	-0.3998	-0.3788	0.1235	0.071	0.086	0.4303	0.2711	0.3932	58.33	61.785	49.165
17	4.7926	-1.2307	-3.7792	11.5904	-3.4917	4.7677	0.7287	0.4434	0.6231	0.7392	-0.0678	0.2188	-0.8679	-0.4563	-0.6609	0.4448	-0.163	0.0322	0.5948	0.3049	0.6258	64.654	58.293	44.287
18	3.8807	4.1971	-4.5384	10.1328	-4.9719	8.4452	-0.0755	-0.4163	-0.0117	-0.262	-0.1872	-0.2052	0.6305	0.4687	0.2627	0.2205	-0.0277	0.0262	0.4117	0.1566	0.456	67.752	50.189	50.894

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	21 - 46
2	X-RAY DIFFRACTION	2	A	47 - 69
3	X-RAY DIFFRACTION	3	A	70 - 77
4	X-RAY DIFFRACTION	4	A	78 - 90
5	X-RAY DIFFRACTION	5	A	98 - 131
6	X-RAY DIFFRACTION	6	A	132 - 155
7	X-RAY DIFFRACTION	7	A	156 - 165
8	X-RAY DIFFRACTION	8	A	166 - 186
9	X-RAY DIFFRACTION	9	A	187 - 205
10	X-RAY DIFFRACTION	10	B	15 - 27
11	X-RAY DIFFRACTION	11	B	28 - 44
12	X-RAY DIFFRACTION	12	B	46 - 74
13	X-RAY DIFFRACTION	13	B	75 - 90
14	X-RAY DIFFRACTION	14	B	96 - 109
15	X-RAY DIFFRACTION	15	B	110 - 134
16	X-RAY DIFFRACTION	16	B	135 - 148
17	X-RAY DIFFRACTION	17	B	167 - 181
18	X-RAY DIFFRACTION	18	B	182 - 206

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