PDB-5ujv: Crystal structure of FePYR1 in complex with abscisic acid

ID or keywords:

Entry

Database: PDB / ID: 5ujv

Title

Crystal structure of FePYR1 in complex with abscisic acid

Components

PYR1

Keywords

abscisic acid binding protein / abscisic acid receptor / turfgrass / drought resistance

Function / homology

Function and homology information

nucleus
Similarity search - Function

Biological species

Festuca elata (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Ren, Z. / Wang, Z. / Zhou, X.E. / Hong, Y. / Cao, M. / Chan, Z. / Liu, X. / Shi, H. / Xu, H.E. / Zhu, J.-K.

Citation

Journal: Sci Rep / Year: 2017
Title: Structure determination and activity manipulation of the turfgrass ABA receptor FePYR1.
Authors: Ren, Z. / Wang, Z. / Zhou, X.E. / Shi, H. / Hong, Y. / Cao, M. / Chan, Z. / Liu, X. / Xu, H.E. / Zhu, J.K.

History

Deposition	Jan 19, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2018	Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2	Mar 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ujv.cif.gz	233.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5ujv.ent.gz	191 KB	Display	PDB format
PDBx/mmJSON format	5ujv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5ujv_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5ujv_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5ujv_validation.xml.gz	22.8 KB	Display
Data in CIF	5ujv_validation.cif.gz	30.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uj/5ujv ftp://data.pdbj.org/pub/pdb/validation_reports/uj/5ujv	HTTPS FTP

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Related structure data

Similar structure data	4dvi-2 4li7-1 4w5i-1 4l09-1 4ufu-2 4i9i-1 4uhg-1 5nut-1 2ov2-1 1g5b-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PYR1

B: PYR1

C: PYR1

hetero molecules

69 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PYR1

hetero molecules

defined by author
23 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: PYR1

hetero molecules

defined by author
23 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: PYR1

hetero molecules

defined by author
23 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

A: PYR1

C: PYR1

hetero molecules

A: PYR1

C: PYR1

hetero molecules

A: PYR1

C: PYR1

hetero molecules

A: PYR1

C: PYR1

hetero molecules

B: PYR1

hetero molecules

B: PYR1

hetero molecules

B: PYR1

hetero molecules

B: PYR1

hetero molecules

defined by software
276 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_575	-x,-y+2,z	1
crystal symmetry operation	7_465	y-1,x+1,-z	1
crystal symmetry operation	8_665	-y+1,-x+1,-z	1
crystal symmetry operation	3_664	-y+3/2,x+3/2,z-1/2	1
crystal symmetry operation	4_354	y-3/2,-x+1/2,z-1/2	1
crystal symmetry operation	5_445	-x-1/2,y-1/2,-z+1/2	1
crystal symmetry operation	6_575	x+1/2,-y+5/2,-z+1/2	1

Unit cell

Length a, b, c (Å)	110.620, 110.620, 124.200
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-1013- HOH

#1: Protein	PYR1 Mass: 22748.518 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Festuca elata (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D1UXN2
#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.: 3 Source method: isolated from a genetically manipulated source Formula: C₁₅H₂₀O₄ / Comment: hormone*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.04 Å³/Da / Density % sol: 59.47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: BIS-TRIS, Ammonium sulfate, Polyethylene glycol monomethyl ether 550

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9778 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 24, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9778 Å / Relative weight: 1
Reflection	Resolution: 2.7→82 Å / Num. obs: 38108 / % possible obs: 96.3 % / Redundancy: 23.2 % / CC_1/2: 0.997 / R_merge(I) obs: 0.298 / Net I/σ(I): 11.7
Reflection shell	Resolution: 2.7→2.76 Å / R_merge(I) obs: 3.935 / CC_1/2: 0.306

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→41.303 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 30.28

	R_factor	Num. reflection	% reflection
R_free	0.2528	1842	4.83 %
R_work	0.2282	-	-
obs	0.2295	38108	94.26 %

Solvent computation

Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å

Refinement step

Cycle: LAST / Resolution: 2.7→41.303 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4347	0	57	39	4443

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4485
X-RAY DIFFRACTION	f_angle_d	0.873	6126
X-RAY DIFFRACTION	f_dihedral_angle_d	9.425	1630
X-RAY DIFFRACTION	f_chiral_restr	0.033	709
X-RAY DIFFRACTION	f_plane_restr	0.005	809

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.7001-2.773	0.3473	139	0.3548	2947	X-RAY DIFFRACTION	99
2.773-2.8546	0.4086	144	0.3648	2939	X-RAY DIFFRACTION	99
2.8546-2.9467	0.3683	174	0.3251	2918	X-RAY DIFFRACTION	99
2.9467-3.052	0.3488	150	0.3033	2947	X-RAY DIFFRACTION	100
3.052-3.1742	0.3861	135	0.3035	2973	X-RAY DIFFRACTION	100
3.1742-3.3186	0.3131	139	0.2949	2939	X-RAY DIFFRACTION	100
3.3186-3.4935	0.3266	94	0.3152	2136	X-RAY DIFFRACTION	72
3.4935-3.7122	0.3338	108	0.2951	2300	X-RAY DIFFRACTION	77
3.7122-3.9986	0.2723	112	0.2478	2368	X-RAY DIFFRACTION	80
3.9986-4.4006	0.2129	146	0.1814	2960	X-RAY DIFFRACTION	100
4.4006-5.0364	0.2006	179	0.1636	2948	X-RAY DIFFRACTION	100
5.0364-6.3417	0.2128	154	0.1882	2938	X-RAY DIFFRACTION	100
6.3417-41.3076	0.1973	168	0.174	2953	X-RAY DIFFRACTION	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	0.0637	0.0692	-0.0141	0.0228	0.0308	0.024	-0.0653	-0.2326	0.5301	-0.0312	0.0917	0.1041	0.083	0.2528	-0.0374	0.5232	0.0413	0.1134	0.3108	-0.0251	0.5121	-12.4041	147.7787	3.2605
2	0.0496	-0.0387	0.0369	0.0278	-0.0119	0.0999	-0.0135	-0.0004	0.3408	-0.1215	-0.0436	0.2264	0.205	0.314	-0.0301	0.291	0.0042	0.0335	0.0737	-0.0664	0.5572	-17.2696	149.6195	3.421
3	0.0076	0.0254	-0.0024	0.0155	0.0174	-0.0101	0.0903	-0.0284	-0.0091	-0.0373	-0.1538	-0.0083	0.1553	0.0191	-0	0.3807	-0.036	0.0839	0.3007	-0.0235	0.3291	-18.4875	139.0915	0.4373
4	0.0043	0.0094	-0.0263	0.0075	0.0073	-0.0054	-0.1104	0.0783	0.0882	0.0334	-0.0854	0.0004	-0.095	0.0607	0	0.7411	-0.0414	0.2926	0.3247	-0.3692	0.7229	-17.9456	159.1264	21.7249
5	0.0101	0.0189	-0.0025	0.0088	0.0105	0.0162	-0.0482	-0.141	0.0422	-0.0479	0.1006	-0.1273	-0.0492	-0.0584	-0.0138	0.6346	0.1233	0.0419	0.7223	-0.3435	0.5961	-20.2546	153.7485	39.538
6	0.0008	-0.0007	-0.0014	-0.0007	-0.0003	-0.0001	0.0069	0.0005	0.0072	0.0202	-0.0139	-0.0099	-0.0034	0.0017	-0	1.0413	0.1617	-0.0303	1.3286	-0.2424	1.1367	-3.9841	144.6976	45.5666
7	-0.0013	-0.0047	0.0041	0.0044	-0.0044	0.002	-0.0242	-0.0823	0.006	-0.0102	0.132	-0.0347	-0.0867	0.0067	0	0.5187	0.2146	-0.0884	0.9469	-0.1728	0.6997	-16.3414	144.9457	39.4592
8	0.0053	0.0019	0.0122	-0.0012	-0.0015	0.0051	-0.0689	-0.033	0.0377	0.0101	0.0141	-0.0554	0.0217	0.0228	0	0.5359	0.0393	0.129	0.4224	-0.2105	0.6167	-17.3749	147.2273	32.6004
9	0.0001	-0	0.0002	0.0001	0.0002	0.0011	0.0086	0.008	0.0077	0.0004	-0.0103	-0.0007	-0.0009	0.003	0	1.4162	0.0687	0.026	1.3508	-0.112	1.3953	-20.4493	177.3758	31.9916
10	0.0077	0.0017	-0.0189	0.0017	0.0041	0.0029	0.1452	-0.089	-0.0389	-0.0131	0.1456	0.0135	0.0081	-0.0271	-0	0.4428	-0.0513	0.384	0.2155	-0.5004	0.6396	-22.6333	147.7701	26.9109
11	0.0214	0.009	-0.0203	0.0064	-0.0125	0.0197	-0.1597	0.0175	0.1291	0.0659	0.0755	-0.0538	-0.0686	-0.0958	-0.0174	0.548	0.0594	0.0923	0.589	-0.4734	0.6055	-27.5367	155.0706	35.4803
12	0.0017	-0.0025	-0.0003	0.0003	-0.0036	0.0058	-0.0708	0.0052	-0.0325	-0.0418	-0.0865	0.0142	-0.0126	0.0745	0	0.3798	-0.0495	0.0018	0.5123	-0.0507	0.3864	6.1894	120.5202	6.5987
13	0.0019	0.0088	0.0589	0.0349	0.0132	0.0191	0.0242	-0.1875	0.2093	0.2742	0.0009	0.2509	-0.1933	0.1041	0.0491	0.4885	0.0525	0.0174	0.4246	-0.2178	0.3693	5.2697	128.6737	26.8627
14	0.0272	0.0036	0.0081	0.0101	-0.0177	0.0042	-0.144	-0.07	-0.0419	0.0797	0.0038	-0.0637	-0.1408	0.0598	-0.0362	0.411	-0.0045	-0.0148	0.3055	-0.1123	0.3336	8.5568	128.79	18.398
15	0.0195	-0.0031	0.0093	0.0026	0.0039	0.0038	0.0335	0.0316	-0.0189	0.0077	0.047	-0.0711	0.0482	0.0916	0	0.4729	-0.0168	-0.054	0.4085	-0.0157	0.5198	15.8074	123.1486	20.9224

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 94 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 95 through 171 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 172 through 202 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 12 through 41 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 42 through 80 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 81 through 94 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 95 through 121 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 122 through 146 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 147 through 154 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 155 through 171 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 172 through 202 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 12 through 33 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 34 through 121 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 122 through 171 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 172 through 202 )

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