PDB-3t4o: Arabidopsis histidine kinase 4 sensor domain in complex with dihy...

ID or keywords:

Entry

Database: PDB / ID: 3t4o

Title

Arabidopsis histidine kinase 4 sensor domain in complex with dihydrozeatin

Components

Histidine kinase 4

Keywords

hormone receptor / sensor histidine kinase /

PAS domain /

endoplasmic reticulum

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: 1.75 Å

Authors

Hothorn, M.

Citation

Journal: Nat.Chem.Biol. / Year: 2011
Title: Structural basis for cytokinin recognition by Arabidopsis thaliana histidine kinase 4.
Authors: Hothorn, M. / Dabi, T. / Chory, J.

History

Deposition	Jul 26, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 5, 2011	Provider: repository / Type: Initial release
Revision 1.1	Dec 14, 2011	Group: Database references
Revision 1.2	Sep 13, 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	3t4o.cif.gz	255.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3t4o.ent.gz	207.9 KB	Display	PDB format
PDBx/mmJSON format	3t4o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t4/3t4o ftp://data.pdbj.org/pub/pdb/validation_reports/t4/3t4o	HTTPS FTP

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Related structure data

Related structure data	3t4jSC 3t4kC 3t4lC 3t4qC 3t4sC 3t4tC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3t4t-d 3t4s-d 3t4j-d 3t4q-d 3t4l-d 3t4k-d 1tu4-7 5fh6-d 3guy-1 1eba-3 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
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: Histidine kinase 4

B: Histidine kinase 4

hetero molecules

62 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)	60.010, 60.010, 297.860
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	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: 30735.533 Da / Num. of mol.: 2 / Fragment: unp residues 149-418 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AHK4, At2g01830, CRE1, RAW1, T23K3.2, WOL / Plasmid: pMH-HSsumo / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) References: UniProt: Q9C5U0, histidine kinase, protein-serine/threonine phosphatase
#2: Chemical	ChemComp-WA2 / (2R)-2-methyl-4-(7H-purin-6-ylamino)butan-1-ol Mass: 221.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O
#3: Chemical	ChemComp-MLI / MALONATE ION / Malonic acid Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₂O₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.52 Å³/Da / Density % sol: 51.16 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 16% PEG 3,350, 0.2 M Na malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99988 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99988 Å / Relative weight: 1
Reflection	Resolution: 1.75→19.69 Å / Num. all: 64550 / Num. obs: 64550 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / R_sym value: 0.067 / Net I/σ(I): 20.15
Reflection shell	Resolution: 1.75→1.79 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.89 / Num. unique all: 4596 / R_sym value: 0.108 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3T4J

3t4j

Resolution: 1.75→19.69 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.955 / SU B: 5.148 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2021	3222	5 %	RANDOM
R_work	0.17943	-	-	-
all	0.18058	61157	-	-
obs	0.18058	61157	99.99 %	-

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: 21.652 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.82 Å²	0.41 Å²	0 Å²
2-	-	0.82 Å²	0 Å²
3-	-	-	-1.22 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→19.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4218	0	39	534	4791

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	4586
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3135
X-RAY DIFFRACTION	r_angle_refined_deg	1.362	1.957	6254
X-RAY DIFFRACTION	r_angle_other_deg	0.914	3	7628
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.511	5	589
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.749	23.636	242
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.929	15	791
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.991	15	41
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	683
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	5208
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	985
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	0.688	1.5	2748
X-RAY DIFFRACTION	r_mcbond_other	0.205	1.5	1096
X-RAY DIFFRACTION	r_mcangle_it	1.188	2	4474
X-RAY DIFFRACTION	r_scbond_it	1.904	3	1838
X-RAY DIFFRACTION	r_scangle_it	2.967	4.5	1747
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.75→1.795 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.31	225	-
R_work	0.264	4423	-
obs	-	-	99.94 %

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	3.5822	3.4417	3.0003	10.1354	-2.61	7.0413	0.5456	-0.0048	-0.0617	1.2771	-0.5289	-0.1437	-0.0735	0.7414	-0.0167	0.3558	0.0227	-0.0145	1.1521	0.0499	0.2463	-4.4041	7.3449	66.9084
2	0.1962	0.0647	-0.9288	0.0753	-1.1022	19.1381	-0.0642	-0.1367	-0.0498	0.0019	-0.0402	0.0085	0.2612	-0.0952	0.1044	0.0825	-0.0331	0.0091	0.2617	0.0393	0.1571	-5.3251	9.927	35.4694
3	2.5116	0.4594	0.3735	1.1523	0.0469	1.1922	0.0994	-0.0758	0.1276	-0.0551	-0.0968	0.0889	-0.0797	-0.2392	-0.0025	0.0489	0.0428	0.0008	0.1826	0.0274	0.1314	-3.5579	19.6416	15.6693
4	5.5031	-1.4233	1.3341	5.2066	-0.0309	11.6583	-0.0042	-0.0076	0.2011	-0.1025	-0.1273	-0.1176	-0.6628	0.132	0.1315	0.0713	0.0082	0.0256	0.1023	0.0324	0.1503	10.6773	29.6054	10.661
5	2.605	0.276	-0.5366	2.1987	0.215	2.1393	-0.0092	-0.1675	0.1519	0.1875	-0.0078	-0.1543	-0.1805	0.1529	0.0169	0.0447	0.0142	-0.0043	0.1797	0.019	0.0933	10.3804	22.2215	20.0538
6	2.2783	-1.0895	-1.6155	3.0296	2.484	4.9911	0.0388	-0.0368	-0.1487	0.1652	-0.1244	0.1457	0.1351	-0.0548	0.0856	0.0195	0.0149	0.0085	0.1658	0.0803	0.1275	7.103	13.3753	22.5991
7	10.0883	6.8743	-12.6632	5.2449	-8.4209	15.9753	0.5142	0.0296	0.4424	0.3455	-0.0221	0.4281	-0.6455	-0.074	-0.492	0.1653	-0.0228	0.0461	0.3417	0.0221	0.232	-6.3255	21.1159	44.3637
8	8.3328	-2.4928	-5.0805	4.3395	2.8832	6.7192	0.0655	-0.5349	0.314	0.2836	0.0503	-0.2324	0.0599	0.4492	-0.1158	0.1555	-0.033	-0.0104	0.3544	0.0651	0.1717	7.6418	15.6788	45.8849
9	2.997	-14.3511	9.9448	83.7358	-59.9166	43.097	0.6247	-0.7991	0.5494	-0.321	0.9802	1.7039	0.0543	-0.0943	-1.6049	1.1622	-0.4248	0.5649	1.8332	-0.7117	1.482	6.0671	18.2721	59.2625
10	4.3906	-1.1618	-6.0479	1.3189	1.1934	13.8957	-0.0356	-0.4514	-0.0651	0.1901	-0.0872	-0.1233	0.4109	0.5256	0.1228	0.0957	-0.0104	-0.001	0.322	0.097	0.164	4.875	9.5174	45.1944
11	5.9347	-0.8102	0.8743	7.5604	-5.8408	14.7422	0.0318	-0.5977	-0.3478	0.4819	0.1729	0.3906	0.2766	-0.1899	-0.2047	0.1479	0.0186	-0.0219	0.2845	0.0395	0.1504	-16.5405	-12.0105	52.9453
12	0.1259	-0.2886	0.0825	12.5715	-13.0878	14.033	-0.0576	-0.1088	0.0223	0.353	-0.1383	-0.2314	-0.2526	0.3471	0.1959	0.0894	-0.0001	-0.0382	0.2758	0.0208	0.1346	-16.3144	4.5266	30.2037
13	3.9037	0.42	-0.1834	2.2954	0.3015	2.2853	0.0989	0.1583	0.0434	-0.2036	-0.1744	-0.1824	-0.048	0.0686	0.0755	0.0298	0.0405	-0.0005	0.2081	0.0296	0.101	-16.0344	10.0222	12.7716
14	5.1833	-0.5648	0.2092	6.6671	-0.8817	6.5659	-0.0483	0.3186	0.1353	-0.6264	0.022	-0.1461	0.0219	0.1657	0.0263	0.0834	0.0461	-0.0185	0.2516	-0.0125	0.0828	-32.3362	8.738	1.5262
15	4.9694	-0.6372	2.2766	1.4011	-0.52	1.1909	0.1747	0.1312	-0.3633	-0.086	-0.0537	0.0514	0.1752	0.0217	-0.121	0.099	0.036	0.0146	0.2727	0.02	0.1102	-30.5797	2.5753	8.3875
16	2.3478	-1.7425	0.5797	4.0748	-1.3517	2.1614	-0.0165	-0.0976	0.0778	0.1985	-0.0101	-0.0204	-0.0104	0.0251	0.0266	0.0235	0.02	-0.0176	0.2473	0.0147	0.0793	-28.8304	7.076	22.0118
17	5.283	-2.0571	1.5601	3.5582	-0.1073	3.0003	0.0809	0.0386	-0.571	0.2328	0.0808	0.3293	0.302	-0.1407	-0.1617	0.2043	0.0246	-0.0169	0.2856	0.0382	0.1911	-26.5955	-9.9112	38.1989
18	1.825	-1.2973	1.5558	2.5366	-1.3808	4.3966	-0.1535	-0.1779	-0.0842	0.4567	0.1977	0.0928	-0.238	-0.2015	-0.0442	0.0905	0.0319	-0.0024	0.2767	0.0523	0.1448	-26.5569	-2.3999	37.2453

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	126 - 135
2	X-RAY DIFFRACTION	2	A	136 - 170
3	X-RAY DIFFRACTION	3	A	171 - 210
4	X-RAY DIFFRACTION	4	A	211 - 228
5	X-RAY DIFFRACTION	5	A	229 - 272
6	X-RAY DIFFRACTION	6	A	273 - 325
7	X-RAY DIFFRACTION	7	A	326 - 339
8	X-RAY DIFFRACTION	8	A	340 - 361
9	X-RAY DIFFRACTION	9	A	364 - 369
10	X-RAY DIFFRACTION	10	A	370 - 393
11	X-RAY DIFFRACTION	11	B	127 - 144
12	X-RAY DIFFRACTION	12	B	145 - 166
13	X-RAY DIFFRACTION	13	B	167 - 206
14	X-RAY DIFFRACTION	14	B	207 - 227
15	X-RAY DIFFRACTION	15	B	228 - 259
16	X-RAY DIFFRACTION	16	B	260 - 333
17	X-RAY DIFFRACTION	17	B	334 - 373
18	X-RAY DIFFRACTION	18	B	374 - 393

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