PDB-3oji: X-ray crystal structure of the Py13 -pyrabactin complex

ID or keywords:

Entry

Database: PDB / ID: 3oji

Title

X-ray crystal structure of the Py13 -pyrabactin complex

Components

Abscisic acid receptor PYL3

Keywords

HORMONE RECEPTOR / ABSCISIC ACID RECEPTOR / CRYSTAL / PP2C / pyl3 / pyrabactin

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: 1.84 Å

Authors

Zhang, X. / Zhang, Q. / 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	Aug 23, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Aug 10, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 6, 2012	Group: Database references
Revision 1.2	Nov 1, 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_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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Download

PDBx/mmCIF format	3oji.cif.gz	171.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3oji.ent.gz	135.9 KB	Display	PDB format
PDBx/mmJSON format	3oji.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3oji_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	3oji_full_validation.pdf.gz	1.3 MB	Display
Data in XML	3oji_validation.xml.gz	22.5 KB	Display
Data in CIF	3oji_validation.cif.gz	34.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/3oji ftp://data.pdbj.org/pub/pdb/validation_reports/oj/3oji	HTTPS FTP

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Related structure data

Related structure data	3kl1C 3klxSC 4ds8C 4dsbC 4dscC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4iz9-d 2e1z-d 4fwn-d 4xh5-d 4fwq-d 4fwp-d 4xh4-d 4fws-d 4xh1-d 4fwo-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: Abscisic acid receptor PYL3

B: Abscisic acid receptor PYL3

hetero molecules

43.6 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)	53.632, 67.538, 109.080
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Abscisic acid receptor PYL3 / PYR1-like protein 3 / Regulatory components of ABA receptor 13 Mass: 21319.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL3 / Plasmid: PGEX 4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2(DE3) / References: UniProt: Q9SSM7
#2: Chemical	ChemComp-PYV / 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide / Pyrabactin Mass: 377.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₁₃BrN₂O₂S
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.32 Å³/Da / Density % sol: 46.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.7M (NH4)2SO4, 100mM cacodylate, 200mM NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 130 K
Diffraction source	Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 29, 2010
Radiation	Monochromator: 0.99 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.83→50 Å / Num. all: 35702 / Num. obs: 32704 / % possible obs: 91.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 5
Reflection shell	Resolution: 1.83→1.86 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.96 / Num. unique all: 1194 / % possible all: 68.1

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
MOLREP		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KLX

3klx

Resolution: 1.84→33.28 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.935 / SU B: 6.96 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 5 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.224	1731	5 %	RANDOM
R_work	0.19947	-	-	-
all	0.20076	35702	-	-
obs	0.20076	32704	97.81 %	-

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: 20.695 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.07 Å²	0 Å²	0 Å²
2-	-	-0.21 Å²	0 Å²
3-	-	-	0.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.84→33.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2841	0	54	576	3471

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	3027
X-RAY DIFFRACTION	r_angle_refined_deg	1.066	1.967	4132
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.517	5	381
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.17	22.941	119
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.946	15	499
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.109	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	495
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	2240
X-RAY DIFFRACTION	r_mcbond_it	0.337	1.5	1886
X-RAY DIFFRACTION	r_mcangle_it	0.629	2	3100
X-RAY DIFFRACTION	r_scbond_it	1.083	3	1141
X-RAY DIFFRACTION	r_scangle_it	1.815	4.5	1032

LS refinement shell

Resolution: 1.838→1.886 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.337	124	-
R_work	0.331	2289	-
obs	-	-	94.93 %

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	7.9783	0.5173	5.4117	3.718	-3.3268	7.2118	0.3234	0.959	0.2379	-0.6309	-0.4103	-0.358	0.5224	0.7973	0.087	0.1452	0.1043	0.0762	0.1828	0.0885	0.0993	-13.082	8.266	-24.306
2	7.1453	-3.63	-3.4937	7.1437	-2.3045	5.2396	0.1161	0.0309	-0.4838	-0.7577	-1.1608	-0.9159	0.7573	1.026	1.0447	0.1527	0.1677	0.1044	0.2697	0.1753	0.2576	-5.203	0.192	-16.367
3	2.0462	-0.7365	0.6684	2.9855	-0.56	0.9964	-0.0375	0.1076	-0.0125	-0.0397	-0.0957	0.0533	-0.0589	-0.0129	0.1331	0.0378	-0.03	0.0139	0.0707	-0.0041	0.0661	-18.185	5.909	-12.338
4	3.0015	0.3181	0.726	1.0139	-0.4535	0.8459	0.0452	-0.2119	0.0391	0.2103	-0.0203	-0.0444	-0.0509	-0.0573	-0.0249	0.1044	-0.0016	-0.0166	0.074	-0.0187	0.1023	-16.862	3.335	3.865
5	2.1754	2.3092	0.1384	2.6971	0.3753	0.7199	0.0652	-0.1649	-0.1548	0.084	-0.0529	-0.188	0.0024	-0.0642	-0.0124	0.0782	0.0088	-0.0231	0.0578	-0.0057	0.1452	-15.468	-5.618	3.146
6	1.2878	-0.0569	0.5259	2.608	-0.8185	0.9453	-0.1106	0.0396	0.0234	-0.1094	-0.0044	-0.2844	-0.0662	0.071	0.115	0.0844	-0.0055	0.0008	0.0529	0.0129	0.1161	-9.909	0.514	-3.519
7	1.2529	-1.7157	0.7491	4.6093	-2.109	1.2411	-0.0587	0.1222	0.0267	0.1161	-0.1037	-0.3381	-0.1156	0.1143	0.1624	0.0826	0.0006	-0.0025	0.0576	0.0203	0.1207	-13.436	4.965	-11.667
8	6.9313	-4.6448	3.4461	9.6592	-4.5639	13.1981	-0.1257	0.3085	0.2224	0.2011	0.172	0.3337	-0.6135	-0.7418	-0.0462	0.0904	0.0078	0.0059	0.1605	0.0623	0.1175	-26.824	20.578	-23.795
9	3.422	-3.1616	1.488	3.6466	-1.9523	1.2885	0.0185	0.2203	-0.2601	-0.0709	-0.0693	-0.2835	0.0833	0.058	0.0508	0.0838	0.0112	0.0374	0.0757	-0.0308	0.1813	-14.279	-8.632	-13.408
10	2.32	-2.1884	-0.3532	8.0595	2.0475	0.9462	0.0861	0.1961	-0.0085	-0.0456	-0.1498	-0.114	-0.0683	-0.0506	0.0637	0.0801	-0.0166	0.0072	0.091	0.0032	0.1088	-23.984	-0.129	-10.266
11	4.5804	-1.7675	-4.282	4.1394	1.7238	7.7495	0.3597	0.3758	0.1133	-0.3557	-0.1364	0.0427	-0.4819	-0.5608	-0.2233	0.1189	0.0719	-0.0307	0.1101	-0.0141	0.0286	-41.016	-6.992	-27.463
12	2.4656	-2.0893	1.5674	14.8187	-0.6898	0.5683	0.1995	0.2894	0.0842	-0.9046	-0.27	0.6168	-0.0721	-0.0461	0.0705	0.115	0.0846	0.0025	0.2575	0.0217	0.1121	-50.291	1.737	-20.145
13	2.1465	-1.373	-1.1314	2.8515	0.5752	0.5468	0.1688	0.1443	0.2495	-0.2893	-0.1008	-0.2092	-0.1053	0.0207	-0.068	0.1056	0.0038	-0.006	0.0754	0.017	0.1037	-37.821	-1.089	-17.647
14	1.0288	0.3039	-0.6073	2.0482	0.6912	0.9255	0.0461	-0.0863	-0.0436	0.1351	-0.0005	0.018	0.0723	0.0099	-0.0456	0.0822	0.0003	-0.0149	0.068	0.0125	0.1248	-37.296	-8.225	-3.626
15	1.5131	1.9113	-3.1304	4.5862	-4.0754	3.8852	0.2649	-0.2636	-0.097	0.4966	-0.2941	-0.0061	-0.0397	0.0642	0.0292	0.1288	-0.0272	0.0066	0.0964	0.0319	0.1818	-48.805	-10.882	4.777
16	2.4352	2.0941	0.4107	1.755	0.8223	1.4841	0.0618	-0.2437	0.1901	0.0221	-0.0518	0.1601	-0.2308	-0.0318	-0.01	0.1211	-0.0129	0.0199	0.0669	0.0028	0.1439	-43.514	2.994	1.174
17	1.2847	0.0577	-0.7959	2.8909	0.7283	1.1067	0.127	0.0479	0.0386	0.0007	-0.0841	0.2246	-0.0682	-0.1631	-0.043	0.08	0.0145	-0.0052	0.0537	-0.0078	0.1185	-47.461	-1.776	-8.568
18	7.6018	-2.2316	-4.6613	8.9259	2.9053	7.7118	-0.1235	-0.1033	-0.2676	-0.0761	0.0463	-0.5338	0.8068	0.6581	0.0772	0.1866	0.082	-0.0035	0.1169	-0.0389	0.1104	-29.408	-21.246	-24.343
19	1.5765	-2.065	-0.4129	5.3163	1.0787	0.8952	0.016	0.1458	0.1621	0.0042	-0.0158	0.0644	-0.0939	0.0006	-0.0002	0.1105	-0.0018	0.0137	0.051	0.0264	0.0851	-40.532	7.154	-15.506
20	1.9998	-2.7843	0.3072	7.5304	-0.711	0.7289	0.1069	0.0645	-0.0463	-0.072	-0.1449	0.0508	0.0315	0.0573	0.038	0.0754	-0.0204	0.0062	0.0759	0.0001	0.1005	-31.702	-4.708	-9.825

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	21 - 36
2	X-RAY DIFFRACTION	2	A	37 - 46
3	X-RAY DIFFRACTION	3	A	48 - 67
4	X-RAY DIFFRACTION	4	A	68 - 99
5	X-RAY DIFFRACTION	5	A	100 - 120
6	X-RAY DIFFRACTION	6	A	121 - 141
7	X-RAY DIFFRACTION	7	A	142 - 155
8	X-RAY DIFFRACTION	8	A	156 - 165
9	X-RAY DIFFRACTION	9	A	166 - 186
10	X-RAY DIFFRACTION	10	A	187 - 206
11	X-RAY DIFFRACTION	11	B	21 - 37
12	X-RAY DIFFRACTION	12	B	38 - 47
13	X-RAY DIFFRACTION	13	B	48 - 60
14	X-RAY DIFFRACTION	14	B	61 - 84
15	X-RAY DIFFRACTION	15	B	85 - 99
16	X-RAY DIFFRACTION	16	B	100 - 120
17	X-RAY DIFFRACTION	17	B	121 - 151
18	X-RAY DIFFRACTION	18	B	152 - 164
19	X-RAY DIFFRACTION	19	B	165 - 187
20	X-RAY DIFFRACTION	20	B	188 - 209

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