PDB-5mn0: ABA RECEPTOR FROM CITRUS, CSPYL1

ID or keywords:

Entry

Database: PDB / ID: 5mn0

Title

ABA RECEPTOR FROM CITRUS, CSPYL1

Components

CSPYL1
Protein phosphatase 2C 16

Keywords

SIGNALING PROTEIN / ABA / RECEPTOR / SIGNALING / STRESS

Function / homology

Function and homology information

abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / signaling receptor activity / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Citrus sinensis (sweet orange)

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Moreno-Alvero, M. / Yunta, C. / Gonzalez-Guzman, M. / Arbona, V. / Granell, A. / Martinez-Ripoll, M. / Infantes, L. / Rodriguez, P.L. / Albert, A.

Citation

Journal: Mol Plant / Year: 2017
Title: Structure of Ligand-Bound Intermediates of Crop ABA Receptors Highlights PP2C as Necessary ABA Co-receptor.
Authors: Moreno-Alvero, M. / Yunta, C. / Gonzalez-Guzman, M. / Lozano-Juste, J. / Benavente, J.L. / Arbona, V. / Menendez, M. / Martinez-Ripoll, M. / Infantes, L. / Gomez-Cadenas, A. / Rodriguez, P.L. / Albert, A.

History

Deposition	Dec 12, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 2, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5mn0.cif.gz	210.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5mn0.ent.gz	166.4 KB	Display	PDB format
PDBx/mmJSON format	5mn0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5mn0_validation.pdf.gz	729.8 KB	Display	wwPDB validaton report
Full document	5mn0_full_validation.pdf.gz	740.4 KB	Display
Data in XML	5mn0_validation.xml.gz	21.2 KB	Display
Data in CIF	5mn0_validation.cif.gz	29.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mn/5mn0 ftp://data.pdbj.org/pub/pdb/validation_reports/mn/5mn0	HTTPS FTP

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Related structure data

Related structure data	5mmqC 5mmxC 5moaC 5mobC C: citing same article (ref.)
Similar structure data	4lg5-d 4ds8-d 4lgb-d 4lga-d 3bex-3 3nmv-d 4oic-d 2ik9-d 3kdj-d 4nir-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: CSPYL1

B: Protein phosphatase 2C 16

hetero molecules

61.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	42.778, 62.679, 187.917
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 2 types, 2 molecules AB

#1: Protein	CSPYL1 Mass: 23294.807 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrus sinensis (sweet orange) / Gene: CISIN_1g046151mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A067E666
#2: Protein	Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1 Mass: 37029.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAB1, P2C-HA, At1g72770, F28P22.4 / Production host: Escherichia coli (E. coli) References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase

#1: Protein

CSPYL1

Mass: 23294.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Citrus sinensis (sweet orange) / Gene: CISIN_1g046151mg / Production host:

Escherichia coli (E. coli) / References: UniProt: A0A067E666

#2: Protein

Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1

Mass: 37029.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: HAB1, P2C-HA, At1g72770, F28P22.4 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase

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Non-polymers , 5 types, 132 molecules

#3: 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.: 1 / Source method: obtained synthetically / Formula: C₁₅H₂₀O₄ / Comment: hormone*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.47 Å³/Da / Density % sol: 50.24 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.5M CaCl2, 0.1 B-T pH7.0, 35% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 35415 / % possible obs: 99.8 % / Redundancy: 13 % / CC_1/2: 0.99 / Net I/σ(I): 13.02
Reflection shell	Resolution: 2→2.12 Å / % possible all: 99

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
Aimless	v1.7	data scaling
SCALA	v1.7	data scaling
MOLREP	v1.7	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→46.979 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 0.5 / Phase error: 33.03

	R_factor	Num. reflection	% reflection
R_free	0.2461	3399	5.13 %
R_work	0.2058	-	-
obs	0.2079	66255	99.73 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2→46.979 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3756	0	34	121	3911

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3849
X-RAY DIFFRACTION	f_angle_d	0.85	5209
X-RAY DIFFRACTION	f_dihedral_angle_d	18.246	2317
X-RAY DIFFRACTION	f_chiral_restr	0.055	588
X-RAY DIFFRACTION	f_plane_restr	0.006	677

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 (%)
1.9952-2.0237	0.5118	93	0.3992	2572	X-RAY DIFFRACTION	96
2.0237-2.0539	0.3588	138	0.3775	2652	X-RAY DIFFRACTION	100
2.0539-2.086	0.4011	114	0.3607	2619	X-RAY DIFFRACTION	100
2.086-2.1202	0.3843	105	0.3654	2665	X-RAY DIFFRACTION	100
2.1202-2.1567	0.3745	153	0.3551	2625	X-RAY DIFFRACTION	100
2.1567-2.1959	0.4434	151	0.3336	2558	X-RAY DIFFRACTION	100
2.1959-2.2382	0.365	138	0.3127	2692	X-RAY DIFFRACTION	100
2.2382-2.2839	0.3703	150	0.2837	2561	X-RAY DIFFRACTION	100
2.2839-2.3335	0.3265	146	0.2774	2615	X-RAY DIFFRACTION	100
2.3335-2.3878	0.3453	159	0.2752	2637	X-RAY DIFFRACTION	100
2.3878-2.4475	0.3009	135	0.2653	2601	X-RAY DIFFRACTION	100
2.4475-2.5137	0.2785	129	0.2605	2697	X-RAY DIFFRACTION	100
2.5137-2.5877	0.3523	127	0.2519	2564	X-RAY DIFFRACTION	100
2.5877-2.6712	0.2984	135	0.2552	2653	X-RAY DIFFRACTION	100
2.6712-2.7666	0.3486	148	0.266	2603	X-RAY DIFFRACTION	100
2.7666-2.8774	0.3144	154	0.2361	2647	X-RAY DIFFRACTION	100
2.8774-3.0083	0.2715	177	0.224	2556	X-RAY DIFFRACTION	100
3.0083-3.1669	0.3029	159	0.2187	2627	X-RAY DIFFRACTION	100
3.1669-3.3653	0.237	129	0.2081	2604	X-RAY DIFFRACTION	100
3.3653-3.625	0.2239	155	0.1771	2634	X-RAY DIFFRACTION	100
3.625-3.9896	0.1969	148	0.1587	2634	X-RAY DIFFRACTION	100
3.9896-4.5665	0.1864	139	0.141	2617	X-RAY DIFFRACTION	100
4.5665-5.7517	0.184	162	0.1492	2604	X-RAY DIFFRACTION	100
5.7517-46.9923	0.1728	155	0.1668	2619	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	0.8273	0.5312	0.0664	1.2045	-0.5547	0.6501	0.1247	-0.2468	-0.1883	0.5021	-0.0926	-0.1155	0.2261	0.0443	0	0.7461	0.0239	-0.0505	0.4613	0.0722	0.4276	4.8794	7.3606	51.3726
2	0.5777	0.5659	-0.1003	0.4439	-0.1771	0.4599	-0.0326	0.098	-0.0119	0.187	0.0149	0.1877	0.4556	-0.1492	-0	0.7669	-0.117	0.0444	0.4656	0.0347	0.4129	-6.2008	0.6961	36.4793
3	1.4744	0.8556	0.5367	0.9924	-0.1645	0.3855	-0.0257	0.0747	-0.1442	0.4623	0.0002	-0.0682	0.603	-0.1611	-0.0006	0.7434	0.0292	0.0009	0.3142	0.0531	0.3574	3.6301	6.7729	43.4299
4	0.1082	0.2043	-0.1644	0.508	-0.6795	0.5694	-0.1133	-0.3113	0.1377	0.265	0.2043	-0.0236	0.172	0.2878	-0.0004	0.5586	-0.0038	0.0051	0.4997	0.0257	0.3875	2.2067	13.6982	39.4971
5	2.0697	-0.0635	-0.3177	0.5519	0.6842	1.9465	0.1855	-0.0592	0.355	0.1413	-0.1719	0.0227	-0.3267	-0.0424	0.0003	0.215	0.0089	0.0455	0.3336	-0.0093	0.3588	-5.5996	29.313	7.0364
6	1.4571	0.0199	0.4789	0.3675	-0.246	0.6243	0.1419	-0.2844	0.4584	0.4412	0.1199	0.3966	-0.2555	-0.2541	-0.0001	0.3543	0.0205	0.1574	0.4279	-0.0897	0.543	-9.4864	36.0249	16.3675
7	0.5825	-0.1879	0.2941	0.3112	0.2308	0.3775	0.1415	-0.3254	0.3496	0.3935	0.06	-0.1531	-0.1866	0.1221	-0.0005	0.5833	-0.1207	0.0903	0.4914	-0.1423	0.5175	-1.1826	37.7733	19.4481
8	0.1582	-0.2585	-0.1116	1.0094	-0.3611	1.907	0.0692	-0.0381	0.094	0.163	-0.0719	-0.0134	-0.1539	0.0088	0.0001	0.2247	-0.0584	0.0194	0.3055	-0.0042	0.3217	5.1046	25.9923	12.488
9	1.1734	1.0739	-0.4035	0.9484	0.3087	0.6927	-0.0736	0.137	0.0709	-0.1851	0.0447	0.0989	-0.0344	-0.1039	0.0001	0.2457	0.0031	-0.0139	0.3251	0.0395	0.3243	-2.7672	21.8617	-4.1674

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 141 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 142 through 181 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 182 through 207 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 186 through 248 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 249 through 272 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 273 through 302 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 303 through 458 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 459 through 505 )

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