PDB-3t4t: Arabidopsis histidine kinase 4 sensor domain in complex with thia...

ID or keywords:

Entry

Database: PDB / ID: 3t4t

Title

Arabidopsis histidine kinase 4 sensor domain in complex with thiadiazuron

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 / cellular response to sucrose stimulus / regulation of seed germination / protein histidine kinase binding / cytokinin-activated signaling pathway ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 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	Jul 25, 2012	Group: Other
Revision 1.3	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
Revision 1.4	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3t4t.cif.gz	256.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3t4t.ent.gz	209.1 KB	Display	PDB format
PDBx/mmJSON format	3t4t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3t4t_validation.pdf.gz	468.4 KB	Display	wwPDB validaton report
Full document	3t4t_full_validation.pdf.gz	475.2 KB	Display
Data in XML	3t4t_validation.xml.gz	27.8 KB	Display
Data in CIF	3t4t_validation.cif.gz	41.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t4/3t4t ftp://data.pdbj.org/pub/pdb/validation_reports/t4/3t4t	HTTPS FTP

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Related structure data

Related structure data	3t4jSC 3t4kC 3t4lC 3t4oC 3t4qC 3t4sC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3t4o-d 3t4j-d 3t4s-d 3t4q-d 3t4l-d 3t4k-d 5fh6-d 5v9t-2 3woh-1 4c2f-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
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)	60.090, 60.090, 297.580
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-WA1 / 1-phenyl-3-(1,2,3-thiadiazol-5-yl)urea / THIDIAZURON Mass: 220.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₈N₄OS
#3: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₂O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.52 Å³/Da / Density % sol: 51.25 %
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: 8.2.2 / Wavelength: 0.99988 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 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: 1.7→19.68 Å / Num. all: 67742 / Num. obs: 67742 / % possible obs: 96.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11 % / R_sym value: 0.046 / Net I/σ(I): 28.27
Reflection shell	Resolution: 1.7→1.74 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 2.99 / Num. unique all: 4853 / R_sym value: 0.762 / % possible all: 94.8

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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: 1.7→19.68 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.956 / SU B: 4.623 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20806	3381	5 %	RANDOM
R_work	0.18184	-	-	-
all	0.18317	64361	-	-
obs	0.18317	64361	96.44 %	-

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: 24.751 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.38 Å²	0.19 Å²	0 Å²
2-	-	0.38 Å²	0 Å²
3-	-	-	-0.56 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→19.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4222	0	37	512	4771

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	4607
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3141
X-RAY DIFFRACTION	r_angle_refined_deg	1.474	1.956	6288
X-RAY DIFFRACTION	r_angle_other_deg	0.918	3	7642
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.64	5	596
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.247	23.659	246
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.322	15	794
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.104	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	686
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	5258
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1000
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	0.718	1.5	2757
X-RAY DIFFRACTION	r_mcbond_other	0.218	1.5	1099
X-RAY DIFFRACTION	r_mcangle_it	1.22	2	4495
X-RAY DIFFRACTION	r_scbond_it	1.985	3	1850
X-RAY DIFFRACTION	r_scangle_it	3.082	4.5	1757
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.287	218	-
R_work	0.263	4569	-
obs	-	-	94.49 %

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	1.4214	-6.2546	8.7706	27.7441	-38.8201	54.3606	-0.4972	0.095	0.0598	2.6024	-0.2002	-0.5135	-3.5732	0.5663	0.6974	0.6218	-0.2019	-0.1834	2.7597	0.0453	0.3284	-4.135	7.276	66.818
2	0.1271	0.0771	-1.0825	0.0724	-1.1314	21.6017	-0.0346	-0.1547	-0.0373	0.0052	-0.0528	-0.0017	0.496	-0.0723	0.0874	0.1888	-0.0346	0.0062	0.3614	0.055	0.1632	-5.147	9.999	35.265
3	2.6304	0.5442	0.3438	1.2748	0.138	1.2457	0.1184	-0.1424	0.1865	-0.021	-0.118	0.1386	-0.0291	-0.2626	-0.0004	0.0439	0.0404	0.0063	0.2067	0.0096	0.1547	-3.541	19.762	15.708
4	5.2359	-0.8988	1.5345	4.6018	0.079	13.0921	-0.0654	-0.1292	0.2434	-0.0213	-0.0671	-0.0778	-0.611	0.119	0.1325	0.0583	0.0219	0.0181	0.1137	0.007	0.1682	10.813	29.721	10.671
5	3.0116	0.2604	-0.5786	2.4802	0.674	2.0598	-0.0095	-0.2748	0.1247	0.2351	-0.0365	-0.0604	-0.1289	0.1538	0.046	0.0539	0.0196	0.0006	0.2188	0.0057	0.1147	10.543	22.251	20.045
6	2.7501	-1.4903	-1.7315	4.093	2.7314	5.6593	-0.0326	-0.17	-0.2089	0.3661	-0.0508	0.2701	0.2544	0.0074	0.0834	0.0426	0.0167	0.0317	0.2113	0.077	0.1721	7.247	13.465	22.492
7	7.8809	7.0382	-11.9111	7.0601	-10.1873	18.2719	0.3843	0.0526	0.3249	0.2796	-0.0268	0.4553	-0.5894	-0.1554	-0.3576	0.2497	-0.0337	0.1137	0.4798	0.0092	0.2823	-6.383	21.007	44.377
8	7.5003	-2.8561	-6.7248	4.6939	4.347	9.3378	0.2565	-0.5257	0.3818	0.2279	-0.092	-0.4123	0.0497	0.5387	-0.1645	0.271	-0.0271	0.0364	0.5007	0.0847	0.2409	7.741	15.77	45.696
9	43.9046	-69.629	48.9371	122.9506	-67.7017	62.433	0.4134	0.6396	0.85	-2.0742	1.0067	-4.131	-0.6386	2.4152	-1.4202	0.4657	-0.5089	0.305	1.5748	-0.1543	1.2576	6.059	18.256	59.056
10	4.4286	-0.6063	-5.944	0.7089	1.0226	15.3178	0.0441	-0.4875	-0.1073	0.1614	-0.1739	-0.1224	0.4113	0.5063	0.1298	0.2245	-0.0091	0.0299	0.4569	0.1134	0.2019	4.993	9.589	45.129
11	6.7194	-0.6671	1.9382	10.5347	-5.6089	14.1838	0.3005	-0.6582	-0.4325	0.9523	0.0405	0.6171	0.0599	-0.2584	-0.3409	0.2883	0.0055	0.0049	0.3602	0.0385	0.1986	-16.488	-11.86	52.767
12	0.2634	-0.9992	0.6407	12.4136	-12.8264	14.1272	-0.1165	-0.1244	-0.0141	0.5397	-0.1009	-0.1612	-0.3362	0.4042	0.2174	0.1768	0.0085	-0.0253	0.3476	0.0043	0.1439	-16.145	4.688	30.072
13	4.5822	0.5475	-0.4772	3.1836	0.1231	2.2607	0.1395	0.1357	0.0783	-0.19	-0.1923	-0.1974	-0.0475	0.117	0.0528	0.0263	0.0431	-0.0073	0.2256	0.011	0.1157	-15.897	10.315	12.696
14	6.5221	-0.3138	-0.1473	6.6496	-0.1729	6.8815	0.0322	0.3225	0.0943	-0.7066	0.0137	-0.1397	0.0106	0.1562	-0.0458	0.0943	0.054	-0.0121	0.235	-0.0165	0.1075	-32.37	9.04	1.519
15	5.8709	-0.854	2.8855	1.7547	-0.8824	1.682	0.1336	0.0243	-0.4418	-0.1489	0.0262	0.0619	0.2108	-0.0147	-0.1598	0.123	0.0452	0.019	0.2687	0.01	0.1306	-30.467	2.834	8.375
16	2.5983	-2.2312	0.5658	5.13	-1.6033	2.5111	-0.0826	-0.1964	0.0708	0.352	0.0858	-0.0068	0.0254	0.0448	-0.0032	0.0494	0.0433	-0.0233	0.2973	-0.0064	0.1051	-28.666	7.319	21.963
17	6.3457	-2.2222	2.0152	3.1869	-0.2245	4.5061	0.1958	0.1524	-0.7918	0.3293	0.0807	0.4684	0.4131	-0.1219	-0.2765	0.3206	0.071	-0.0158	0.3894	0.0347	0.2707	-26.35	-9.736	37.988
18	1.8428	-1.4013	3.1259	2.4563	-4.0953	7.8263	-0.0728	-0.1524	-0.1893	0.4639	0.1915	0.1912	-0.4127	-0.2639	-0.1187	0.2843	0.0996	0.1031	0.3575	0.0474	0.2653	-26.395	-2.14	37.397

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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