PDB-7p8d: Crystal structure of the Receiver domain of A. thaliana cytokinin...

ID or keywords:

Entry

Database: PDB / ID: 7p8d

Title

Crystal structure of the Receiver domain of A. thaliana cytokinin receptor AtCRE1 in complex with Mg2+

Components

Receiver domain of histidine kinase 4

Keywords

SIGNALING PROTEIN / flavodoxin-like fold / cytokinin / phosphorelay

Function / homology

Function and homology information

cytokinin receptor activity / transmembrane histidine kinase cytokinin receptor activity / embryonic root morphogenesis / regulation of shoot system development / regulation of meristem development / carbohydrate homeostasis / regulation of seed germination / sulfate transport / cellular response to sucrose stimulus / protein histidine kinase binding ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Tran, L.H. / Urbanowicz, A. / Jasinski, M. / Jaskolski, M. / Ruszkowski, M.

Funding support

Poland, 1items

Citation

Journal: Front Plant Sci / Year: 2021
Title: 3D Domain Swapping Dimerization of the Receiver Domain of Cytokinin Receptor CRE1 From Arabidopsis thaliana and Medicago truncatula .
Authors: Tran, L.H. / Urbanowicz, A. / Jasinski, M. / Jaskolski, M. / Ruszkowski, M.

History

Deposition	Jul 21, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 20, 2021	Provider: repository / Type: Initial release
Revision 1.1	Feb 2, 2022	Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.2	May 1, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7p8d.cif.gz	125.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7p8d_validation.pdf.gz	739.4 KB	Display	wwPDB validaton report
Full document	7p8d_full_validation.pdf.gz	739.6 KB	Display
Data in XML	7p8d_validation.xml.gz	13.6 KB	Display
Data in CIF	7p8d_validation.cif.gz	19.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p8/7p8d ftp://data.pdbj.org/pub/pdb/validation_reports/p8/7p8d	HTTPS FTP

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Related structure data

Related structure data	7p8cC 7p8eC C: citing same article (ref.)
Similar structure data	1ijk-d 2eax-d 3agk-d 1u0o-d 1rj2-3 5dps-d 4bu2-d 6es1-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
Experimental dataset #1	Data reference: 10.18150/UUYPCU / Data set type: diffraction image data / Metadata reference: 10.18150/UUYPCU

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (13) #183 - Mar 2015 Phototropin similarity (8) #151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Receiver domain of histidine kinase 4

B: Receiver domain of histidine kinase 4

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	88.183, 99.202, 35.623
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Receiver domain of histidine kinase 4 / Arabidopsis histidine kinase 4 / AtHK4 / Cytokinin receptor CYTOKININ RESPONSE 1 / AtCRE1 / ...Arabidopsis histidine kinase 4 / AtHK4 / Cytokinin receptor CYTOKININ RESPONSE 1 / AtCRE1 / Cytokinin receptor CRE1 / Phosphoprotein phosphatase AHK4 / Protein AUTHENTIC HIS-KINASE 4 / Protein ROOT AS IN WOL 1 / Protein WOODEN LEG Mass: 15884.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AHK4, CRE1, RAW1, WOL, At2g01830, T23K3.2 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9C5U0, histidine kinase, protein-serine/threonine phosphatase
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 52.99 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.03 M MgCl2, 0.03 M CaCl2 in 0.1 M MES/Imidazole at pH 6.5 and 12.5% of each PEG1000, PEG3350 and 27.5% MPD

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.7→43.23 Å / Num. obs: 35267 / % possible obs: 99.9 % / Redundancy: 12.9 % / B_iso Wilson estimate: 32.44 Å² / CC_1/2: 1 / R_merge(I) obs: 0.057 / R_rim(I) all: 0.059 / Net I/σ(I): 22.9
Reflection shell	Resolution: 1.7→1.8 Å / Redundancy: 13.2 % / R_merge(I) obs: 1.34 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 5583 / CC_1/2: 0.72 / R_rim(I) all: 1.39 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AtCRE1-REC-K

Resolution: 1.7→43.23 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 25.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2456	1058	3 %
R_work	0.1937	-	-
obs	0.1953	35263	99.94 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.7→43.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2076	0	14	182	2272

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2122
X-RAY DIFFRACTION	f_angle_d	1.07	2858
X-RAY DIFFRACTION	f_dihedral_angle_d	16.004	801
X-RAY DIFFRACTION	f_chiral_restr	0.067	323
X-RAY DIFFRACTION	f_plane_restr	0.007	366

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 (%)
1.7-1.78	0.3216	129	0.2684	4186	X-RAY DIFFRACTION	100
1.78-1.87	0.2894	130	0.2423	4212	X-RAY DIFFRACTION	100
1.87-1.99	0.2678	131	0.2218	4219	X-RAY DIFFRACTION	100
1.99-2.14	0.261	131	0.2067	4226	X-RAY DIFFRACTION	100
2.14-2.36	0.2651	131	0.1925	4242	X-RAY DIFFRACTION	100
2.36-2.7	0.2486	132	0.2069	4280	X-RAY DIFFRACTION	100
2.7-3.4	0.2649	134	0.1994	4326	X-RAY DIFFRACTION	100
3.4-43.23	0.2214	140	0.1758	4514	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	4.8636	0.6394	-0.1382	8.8642	-1.0581	4.9822	-0.1942	-0.2491	0.3104	-0.0781	0.4212	0.02	-0.6538	0.3528	-0.2465	0.344	0.0174	0.0381	0.297	-0.0364	0.1889	5.0591	26.6666	18.1098
2	3.1209	-1.9825	1.0353	6.5315	-1.7528	4.1449	-0.0207	-0.3354	-0.0851	0.588	0.0789	0.0404	-0.106	-0.045	-0.0317	0.3036	0.0121	0.0574	0.3389	0.0173	0.2378	3.5183	22.0782	20.6167
3	4.3094	-2.4316	-0.1983	7.4455	0.1866	5.5471	-0.1755	-0.0706	-0.2813	0.2717	0.3759	0.5799	0.1992	-0.1076	-0.1755	0.2583	0.0306	0.0261	0.2764	0.0711	0.2636	-3.1713	22.2576	13.305
4	7.181	-2.3135	1.4956	2.643	-0.5729	0.9681	0.3347	0.3298	-1.0209	-0.2628	-0.2848	1.4698	0.0678	-0.2741	-0.0335	0.2778	0.0351	-0.0527	0.403	-0.0339	0.4712	-10.483	26.5696	5.507
5	8.0927	-5.8643	2.1082	7.388	-2.2102	4.9041	0.355	0.3649	0.3085	-0.4376	-0.3429	-0.2368	0.1735	0.0597	0.01	0.2356	-0.0052	-0.0101	0.2467	0.0125	0.2164	-2.1618	29.9702	7.604
6	5.0964	-4.5009	-2.0312	4.1345	2.1105	2.761	-0.1701	-1.0623	0.2724	0.8989	0.253	-0.1076	-0.1761	-0.1574	0.0551	0.4148	0.0932	0.076	0.5008	0.0507	0.3784	13.2479	5.175	6.8046
7	9.2822	6.3503	-6.1914	4.796	-5.6383	8.7912	0.2459	0.5507	0.5154	-0.4121	0.3403	0.5755	-0.6544	-0.4065	-0.5374	0.4096	0.1095	0.051	0.4088	0.0185	0.3932	20.6544	7.7434	-2.3419
8	6.5404	1.2921	3.1766	4.2019	3.2318	3.2811	0.4187	-0.4497	-0.106	0.6374	-1.7819	-1.2908	1.7049	2.3065	0.8319	0.7603	0.0546	0.0532	1.0138	0.329	0.5733	19.0649	20.3324	-19.2939
9	2.7575	1.8969	2.2522	6.0107	3.1328	4.4571	-0.4346	-0.0074	0.8795	-0.1916	0.5133	0.223	-1.9414	0.0609	0.0405	0.6241	-0.0858	0.0377	0.4382	-0.0668	0.4598	9.1044	32.3742	-33.8879
10	9.7326	6.3714	1.5082	6.1422	3.9864	5.2149	-0.1185	0.1538	-1.0629	0.4023	0.0451	-0.8589	0.2234	0.4886	0.0106	0.2908	-0.0228	0.0412	0.3448	0.0488	0.4864	34.2286	4.3435	-12.5355
11	8.1689	-1.0546	2.3101	4.4723	-1.1018	4.3029	-0.1425	0.3899	-0.1289	-0.2228	0.0703	0.0864	-0.3207	0.1041	0.0754	0.2785	-0.0067	-0.0052	0.2253	-0.0295	0.206	19.4675	4.2915	-15.6987
12	5.3606	-5.1411	0.4048	6.8457	0.2525	4.7411	-0.0543	0.1179	-0.9156	-0.2821	0.0674	0.8775	0.4773	-0.2401	0.001	0.3272	-0.0488	0.0394	0.2552	-0.0158	0.4354	19.3698	-9.2585	-11.6979
13	6.1587	-1.911	-2.5025	7.8514	0.592	6.5661	0.1447	-0.2183	-0.3481	-0.0255	-0.084	0.8696	-0.1817	-0.6717	-0.0669	0.2742	0.0281	0.0095	0.3256	0.0356	0.3918	11.6441	-0.6589	-6.51
14	6.5533	-6.8533	0.0137	8.3562	-0.2668	2.3371	-0.2892	-0.257	-0.8759	0.3429	0.3264	0.8167	0.3709	-0.0232	-0.0316	0.3676	0.0192	0.1136	0.3106	0.0632	0.4223	21.3765	-10.0299	-1.3067
15	8.7194	-4.3367	-1.7728	5.2933	-0.5329	4.5388	0.0206	0.057	-0.1892	-0.4369	-0.1522	-0.1362	0.1955	0.0215	0.0641	0.3061	0.0465	-0.0181	0.2854	0.0037	0.2514	5.9895	18.1471	0.765
16	4.1463	-0.3109	-2.3962	4.9798	4.2219	5.4776	-0.443	-0.7387	1.4947	0.7881	0.2548	0.0341	-0.4797	-0.5132	0.1406	0.4962	0.0633	0.0006	0.6011	0.0404	0.765	21.1941	11.7505	3.7476

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 917 through 930 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 931 through 960 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 961 through 980 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 981 through 999 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1000 through 1011 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1012 through 1025 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1026 through 1035 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 1036 through 1045 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1046 through 1055 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 916 through 922 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 923 through 951 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 952 through 968 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 969 through 980 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 981 through 1011 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 1012 through 1033 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 1034 through 1042 )

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