PDB-3t4j: Arabidopsis histidine kinase 4 sensor domain in complex with N-is...

ID or keywords:

Entry

Database: PDB / ID: 3t4j

Title

Arabidopsis histidine kinase 4 sensor domain in complex with N-isopentenyl adenine

Components

Histidine kinase 4

Keywords

hormone receptor / sensor histidine kinase / PAS domain / family 1 sensor domain / cytokinin binding / 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 ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 1.65 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	Oct 9, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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	3t4j.cif.gz	253.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3t4j.ent.gz	206.8 KB	Display	PDB format
PDBx/mmJSON format	3t4j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3t4j_validation.pdf.gz	461.9 KB	Display	wwPDB validaton report
Full document	3t4j_full_validation.pdf.gz	468.7 KB	Display
Data in XML	3t4j_validation.xml.gz	27.4 KB	Display
Data in CIF	3t4j_validation.cif.gz	41.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t4/3t4j ftp://data.pdbj.org/pub/pdb/validation_reports/t4/3t4j	HTTPS FTP

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Related structure data

Related structure data	3t4kC 3t4lC 3t4oC 3t4qC 3t4sC 3t4tC C: citing same article (ref.)
Similar structure data	3t4t-d 3t4o-d 3t4q-d 3t4s-d 3t4l-d 3t4k-d 5fh6-d 5v9t-2 1eba-3 1vk9-2 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)	59.870, 59.870, 297.340
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-ZIP / N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE / ISOPENTENYLADENINE Mass: 203.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅
#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.: 543 / 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: 2.5 Å³/Da / Density % sol: 50.85 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 19% 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: 1.65→19.8 Å / Num. all: 76048 / Num. obs: 76048 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / R_sym value: 0.042 / Net I/σ(I): 30.64
Reflection shell	Resolution: 1.65→1.69 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 5521 / R_sym value: 0.703 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

SIRAS / Resolution: 1.65→19.8 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.957 / SU B: 3.768 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20077	3793	5 %	RANDOM
R_work	0.17557	-	-	-
all	0.17683	72254	-	-
obs	0.17683	72254	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: 20.549 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.58 Å²	0.29 Å²	0 Å²
2-	-	0.58 Å²	0 Å²
3-	-	-	-0.88 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→19.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4204	0	37	543	4784

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	4543
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3088
X-RAY DIFFRACTION	r_angle_refined_deg	1.358	1.957	6193
X-RAY DIFFRACTION	r_angle_other_deg	0.893	3	7512
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.458	5	580
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.215	23.613	238
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.903	15	781
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.417	15	40
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	678
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	5142
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	974
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	0.637	1.5	2724
X-RAY DIFFRACTION	r_mcbond_other	0.195	1.5	1086
X-RAY DIFFRACTION	r_mcangle_it	1.116	2	4436
X-RAY DIFFRACTION	r_scbond_it	1.915	3	1819
X-RAY DIFFRACTION	r_scangle_it	3.031	4.5	1727
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.65→1.693 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.268	280	-
R_work	0.258	5198	-
obs	-	-	99.98 %

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	2.353	6.6172	2.6368	21.2364	-12.9065	25.9373	0.6746	-0.0474	-0.1267	2.1116	-0.5082	-0.2749	-0.5907	1.4751	-0.1664	0.3455	-0.0105	-0.0145	1.6448	0.1681	0.1446	-4.245	7.339	66.823
2	0.1962	0.0753	-1.1926	0.07	-1.3805	23.0733	-0.0544	-0.1435	-0.0669	-0.0035	-0.0236	0.0086	0.3347	0.0141	0.0781	0.109	-0.0325	0.0143	0.2162	0.0381	0.1246	-5.097	9.946	35.281
3	2.7025	0.4383	0.3679	1.1187	0.0605	1.2977	0.0985	-0.0637	0.1345	-0.0355	-0.095	0.0672	-0.0394	-0.2389	-0.0035	0.05	0.026	0.0036	0.1393	0.0215	0.1014	-3.494	19.595	15.707
4	5.1395	-1.4696	0.6292	5.0126	-0.4482	12.18	-0.0333	0.007	0.2376	-0.0822	-0.0813	-0.0514	-0.5867	0.2288	0.1146	0.0824	0.0084	0.0215	0.0758	0.0248	0.1209	10.786	29.629	10.65
5	2.9496	0.3984	-0.6284	2.0885	0.4869	2.0308	0.0033	-0.1671	0.1704	0.1766	-0.0345	-0.1883	-0.1512	0.1474	0.0312	0.0541	0.0097	-0.0094	0.141	0.0157	0.0742	10.529	22.206	20.026
6	2.4103	-1.2319	-1.7643	2.9301	2.4681	5.0984	0.001	-0.0433	-0.1602	0.1872	-0.0789	0.1217	0.1805	-0.021	0.0779	0.0177	0.0062	0.0076	0.1271	0.062	0.1047	7.248	13.407	22.549
7	13.7117	10.0109	-15.8165	8.3395	-10.8825	18.2964	0.5008	0.2203	0.5723	0.408	0.109	0.4563	-0.5719	-0.3236	-0.6098	0.1632	-0.003	0.0517	0.3153	0.0146	0.1772	-6.28	21.045	44.37
8	9.5768	-3.0096	-6.6096	4.8415	3.6949	8.09	0.0564	-0.6857	0.3464	0.2879	0.0486	-0.283	0.0094	0.6035	-0.105	0.1807	-0.0267	-0.0026	0.3638	0.0585	0.1355	7.808	15.772	45.802
9	-2.6164	-0.8675	-2.3617	89.1342	-52.7522	75.9577	0.5862	-0.5948	0.6705	-1.0918	1.7679	1.0024	-0.5197	1.9607	-2.3541	0.7879	-0.8554	0.5212	1.3708	-0.532	1.1678	6.061	18.215	59.18
10	4.9243	-0.7159	-6.2989	1.2208	0.7761	13.491	0.0161	-0.5616	-0.1345	0.2005	-0.1026	-0.1567	0.4	0.5891	0.0865	0.12	-0.011	-0.0062	0.3291	0.0928	0.1326	4.989	9.582	45.144
11	6.4412	-0.4195	1.6037	7.5869	-6.6929	17.4389	0.0942	-0.6614	-0.3787	0.4398	0.165	0.2971	0.3	-0.2331	-0.2591	0.1641	0.0141	-0.0174	0.2441	0.0389	0.126	-16.365	-11.917	52.831
12	0.0529	-0.2628	0.1738	13.8325	-14.2086	14.6562	-0.0602	-0.0765	0.0173	0.317	-0.1691	-0.2513	-0.2343	0.2682	0.2293	0.1196	-0.0083	-0.0376	0.2341	0.0115	0.0928	-16.151	4.594	30.099
13	4.0408	0.3511	-0.1255	2.8361	-0.1668	2.2899	0.1086	0.1265	0.0468	-0.1292	-0.1812	-0.1534	-0.0432	0.0876	0.0726	0.0167	0.0239	-0.0083	0.1629	0.0175	0.0663	-15.859	10.092	12.705
14	5.1856	-0.6107	0.8491	7.2225	-0.4563	6.6509	-0.0473	0.3617	0.1556	-0.5435	0.0672	-0.0878	-0.0644	0.1352	-0.0199	0.0634	0.037	-0.0206	0.2135	-0.0065	0.0591	-32.272	8.889	1.473
15	4.9198	-0.8573	2.4244	1.831	-0.7478	1.5488	0.1176	0.0944	-0.3716	-0.0717	-0.0098	0.0871	0.208	-0.0151	-0.1078	0.0828	0.0223	0.0174	0.2051	-0.0008	0.0861	-30.4	2.691	8.368
16	2.6507	-2.0052	0.7045	4.5095	-1.5205	2.1615	-0.0511	-0.1201	0.1111	0.2803	0.0301	-0.0176	-0.0465	-0.0099	0.021	0.0319	0.0092	-0.0165	0.2073	0.0038	0.0518	-28.577	7.191	21.948
17	5.7852	-2.3024	2.2509	3.4367	-0.9155	3.924	0.0968	0.0876	-0.648	0.3173	0.1196	0.3952	0.3085	-0.138	-0.2163	0.2233	0.0199	-0.0183	0.252	0.0197	0.1827	-26.413	-9.837	38.069
18	2.2896	-1.5972	2.5866	2.5909	-2.6966	5.809	-0.1773	-0.2294	-0.1006	0.543	0.2749	0.2026	-0.2248	-0.2978	-0.0976	0.1595	0.0407	0.025	0.2356	0.0447	0.1256	-26.363	-2.376	37.539

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	128 - 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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