PDB-5xua: The ligand-free dimer of chemoreceptor MCP2201 ligand binding domain

ID or keywords:

Entry

Database: PDB / ID: 5xua

Title

The ligand-free dimer of chemoreceptor MCP2201 ligand binding domain

Components

Methyl-accepting chemotaxis sensory transducer

Keywords

SIGNALING PROTEIN /

methyl-accepting chemotaxis protein / four helix bundle / dicarboxylic organic acid binding

Function / homology

Function and homology information

chemotaxis / transmembrane signaling receptor activity /

signal transduction /

membrane
Similarity search - Function

Biological species

Comamonas testosteroni (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Hong, Y. / Li, D.F. / Wang, D.C.

Citation

Journal: Mol.Microbiol. / Year: 2019
Title: The ligand-binding domain of a chemoreceptor from Comamonas testosteroni has a previously unknown homotrimeric structure.
Authors: Hong, Y. / Huang, Z. / Guo, L. / Ni, B. / Jiang, C.Y. / Li, X.J. / Hou, Y.J. / Yang, W.S. / Wang, D.C. / Zhulin, I.B. / Liu, S.J. / Li, D.F.

History

Deposition	Jun 23, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 27, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 10, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5xua.cif.gz	426 KB	Display	PDBx/mmCIF format
PDB format	pdb5xua.ent.gz	356 KB	Display	PDB format
PDBx/mmJSON format	5xua.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/xu/5xua ftp://data.pdbj.org/pub/pdb/validation_reports/xu/5xua	HTTPS FTP

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Related structure data

Related structure data	5xubC 6itsC 5xud PDB Unreleased entryS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2rnf-d 3rh3-1 2j12-d 4xh3-d 2z1u-d 3b7l-d 6q2k-d 6vme-5 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5xubC

6itsC

5xud
PDB Unreleased entryS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#158 - Feb 2013 Proton-Gated Urea Channel similarity (8) #190 - Oct 2015 Two-component Systems similarity (4)

Deposited unit

A: Methyl-accepting chemotaxis sensory transducer

B: Methyl-accepting chemotaxis sensory transducer

C: Methyl-accepting chemotaxis sensory transducer

D: Methyl-accepting chemotaxis sensory transducer

E: Methyl-accepting chemotaxis sensory transducer

F: Methyl-accepting chemotaxis sensory transducer

G: Methyl-accepting chemotaxis sensory transducer

H: Methyl-accepting chemotaxis sensory transducer

136 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Methyl-accepting chemotaxis sensory transducer

B: Methyl-accepting chemotaxis sensory transducer

defined by author&software
Evidence: gel filtration
33.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Methyl-accepting chemotaxis sensory transducer

D: Methyl-accepting chemotaxis sensory transducer

defined by author&software
33.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Methyl-accepting chemotaxis sensory transducer

F: Methyl-accepting chemotaxis sensory transducer

defined by author&software
33.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Methyl-accepting chemotaxis sensory transducer

H: Methyl-accepting chemotaxis sensory transducer

defined by author&software
33.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.780, 105.030, 91.070
Angle α, β, γ (deg.)	90.00, 90.95, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Methyl-accepting chemotaxis sensory transducer Mass: 16958.246 Da / Num. of mol.: 8 / Fragment: UNP residues 57-203 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Comamonas testosteroni (bacteria) / Strain: CNB-2 / Gene: CtCNB1_2201 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0IVL9

#1: Protein

Methyl-accepting chemotaxis sensory transducer

Mass: 16958.246 Da / Num. of mol.: 8 / Fragment: UNP residues 57-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Comamonas testosteroni (bacteria) / Strain: CNB-2 / Gene: CtCNB1_2201 / Plasmid: pET22b / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0IVL9

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.13 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.4 Details: 0.1 M BIS-TRIS propane pH 9.4 20% PEG 5,000 MME 2-5% 2-Propanol, 2-5% Glycerol

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.8→55.13 Å / Num. obs: 30025 / % possible obs: 99.5 % / Redundancy: 3.6 % / B_iso Wilson estimate: 70.566 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.107 / Net I/σ(I): 7.7
Reflection shell	Resolution: 2.8→2.95 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.643 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4389 / CC_1/2: 0.7 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
iMOSFLM		data processing
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5XUD

5xud
PDB Unreleased entry

Resolution: 2.8→53.199 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.61

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2663	1447	5.05 %	Random
R_work	0.2219	-	-	-
obs	0.2241	28676	95.12 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→53.199 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8363	0	0	0	8363

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	8435
X-RAY DIFFRACTION	f_angle_d	0.752	11412
X-RAY DIFFRACTION	f_dihedral_angle_d	14.578	5354
X-RAY DIFFRACTION	f_chiral_restr	0.042	1409
X-RAY DIFFRACTION	f_plane_restr	0.005	1456

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 (%)
2.8001-2.9001	0.321	135	0.3077	2424	X-RAY DIFFRACTION	85
2.9001-3.0163	0.3713	136	0.3069	2534	X-RAY DIFFRACTION	89
3.0163-3.1535	0.3273	133	0.297	2631	X-RAY DIFFRACTION	92
3.1535-3.3197	0.3782	146	0.2862	2693	X-RAY DIFFRACTION	95
3.3197-3.5277	0.321	143	0.2529	2762	X-RAY DIFFRACTION	97
3.5277-3.8	0.2668	130	0.2238	2837	X-RAY DIFFRACTION	98
3.8-4.1823	0.2457	157	0.2059	2818	X-RAY DIFFRACTION	99
4.1823-4.7871	0.2487	154	0.1872	2831	X-RAY DIFFRACTION	99
4.7871-6.0299	0.251	154	0.2093	2794	X-RAY DIFFRACTION	98
6.0299-53.2082	0.2021	159	0.1795	2905	X-RAY DIFFRACTION	99

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	2.9965	-0.0615	1.1185	3.237	0.1428	4.1452	-0.2786	-0.1129	0.0571	-0.3851	0.1306	-1.4791	0.3061	0.0569	-0.0686	0.4107	-0.0588	0.075	0.2932	-0.1169	0.4353	8.5365	20.5615	28.0034
2	1.8601	-0.5357	2.1692	3.7431	0.071	8.1075	0.768	0.2778	-0.5525	0.4127	0.7586	-1.391	1.4319	0.0301	-0.006	0.4618	0.0929	-0.1759	0.6137	-0.3378	0.7596	12.4548	12.4733	29.9364
3	4.2998	-0.3872	2.7042	3.9254	0.2226	9.6026	0.1567	0.2466	-0.3326	0.0816	0.0674	-0.148	0.4561	-0.3184	-0.2563	0.4473	-0.0253	-0.0494	0.4489	-0.1236	0.3294	-4.9823	13.8289	22.8949
4	3.1926	0.6355	4.383	0.8733	-0.2912	7.0235	-0.0366	-0.6455	0.3468	0.5472	-0.1315	-0.4609	-0.0348	-0.4905	0.0994	0.6965	-0.018	-0.2347	0.4858	-0.0549	0.4549	5.6645	18.9441	43.9213
5	2.2758	0.5394	2.4809	2.9679	-0.4521	4.1321	-0.0493	-0.2236	0.3901	0.0928	-0.0977	-0.241	0.0427	-0.1382	0.0539	0.3785	0.038	0.025	0.4616	-0.0702	0.4403	8.3812	32.813	32.5405
6	2.9368	0.3619	3.9663	4.2083	-1.268	6.6949	0.0351	-0.5329	-0.0345	-0.2029	0.096	-0.5236	-0.3082	-0.3252	0.0502	0.3939	-0.0277	0.1633	0.5301	0.014	0.4771	15.2208	40.9206	24.6938
7	2.6077	0.9797	-0.0618	3.9754	0.2336	2.7404	-0.6511	0.3704	0.2957	-0.37	-0.0553	-1.084	-0.9485	0.0846	0.229	0.3949	0.0698	0.0607	0.4792	-0.0857	0.4879	17.2665	32.2754	25.5186
8	2.317	0.6111	0.0171	1.2758	0.2022	4.1915	-0.1514	0.4027	0.5605	0.1292	-0.127	0.1119	0.549	0.131	0.2519	0.4047	0.0075	-0.0551	0.3376	0.0274	0.4746	-18.6135	12.9328	47.8396
9	2.6911	-0.6318	1.9669	2.6528	-2.3108	2.9133	-0.9052	0.2073	-0.0268	0.3136	-0.7941	-1.0646	0.1889	1.3073	1.0984	0.616	0.1599	-0.1296	0.5672	-0.1135	0.4676	-13.2451	6.7274	51.8086
10	2.886	0.3518	3.8264	2.0695	2.3815	6.6476	0.2922	0.1302	-0.3048	0.5884	0.1283	0.1364	0.5882	0.2471	-0.3073	0.4413	-0.0244	0.109	0.4619	0.1384	0.451	-26.5335	2.0072	50.5548
11	2.604	-2.7279	-0.5218	5.7024	4.2559	4.8373	0.0599	0.5322	-0.7884	0.5719	-1.308	1.5714	1.1419	-1.1287	0.2893	0.4539	0.0039	0.0141	0.7589	-0.0774	0.9825	-38.4919	3.4603	36.9927
12	5.7304	2.4056	3.4333	3.714	3.6386	7.0389	0.1769	-1.225	0.3421	0.3612	-0.3906	0.3164	0.3429	-0.3489	0.2903	0.5118	0.0272	0.1117	0.5031	-0.0014	0.3249	-22.2293	14.1855	61.399
13	3.9535	1.2763	3.9199	4.6091	3.8367	7.8313	0.2305	-0.4547	0.364	0.5836	-0.1741	0.6283	0.7417	-0.4428	-0.0195	0.3678	-0.0386	-0.0109	0.4995	0.0241	0.4106	-17.2651	24.4748	51.7398
14	2.7633	1.5282	-1.4624	5.6885	1.0916	4.0691	0.8855	-0.0803	-0.0897	0.5837	0.0389	2.076	-0.2661	-1.4293	-0.0709	0.9694	0.2766	-0.2389	0.6373	0.0038	1.1455	-24.9308	27.2476	46.1139
15	6.5915	1.431	4.1857	5.7843	0.1893	4.0142	-0.3375	-0.0454	1.2527	-0.3309	0.1746	0.4364	-1.2905	-0.3923	0.0007	0.4888	0.0629	0.2141	0.4792	0.0336	0.5296	-16.07	32.6652	38.8129
16	1.5344	0.8287	0.9022	3.4991	0.9015	9.5225	0.3458	0.255	-0.2227	0.1074	0.3925	-0.0783	0.2808	0.668	-0.8192	0.3845	0.0674	-0.0086	0.4648	-0.061	0.4328	-12.2829	25.1208	41.7354
17	1.6916	-0.8077	2.0576	0.4908	-1.4614	3.9561	-0.7106	0.1805	0.9719	-0.1628	0.0656	0.7273	-1.6945	-0.2008	-0.3194	1.0259	-0.0683	-0.3166	0.5975	0.325	0.7111	-21.544	56.9609	12.0029
18	6.5067	-0.5091	3.6982	0.9068	-1.6692	6.0259	-0.5445	-0.8614	1.6866	-0.3491	0.5801	2.0592	-1.4395	0.9764	0.8563	0.8983	0.388	-0.3593	0.2953	-0.0087	0.9714	-22.4155	59.2997	21.8574
19	2.1482	1.284	1.0076	1.9271	1.8119	3.9141	-0.6271	-0.5557	0.0693	-0.1058	0.0471	1.159	-1.0658	-1.2087	0.6724	0.5567	0.196	-0.0273	0.6392	0.0514	0.8363	-30.2972	48.9328	23.4648
20	0.1479	-0.6318	1.0761	3.1021	-2.7765	5.8581	-0.4904	-0.0323	0.4569	-0.0622	0.3278	0.6126	-0.4468	-0.8158	0.1595	0.5516	-0.004	-0.1056	0.5762	0.2537	0.6585	-24.5606	46.742	15.0163
21	1.9309	0.1198	-0.1804	1.6086	0.1456	0.0579	-0.2826	0.6449	0.26	-0.6984	-0.0359	0.1802	0.171	0.1905	0.1772	0.836	-0.1737	-0.1629	0.6944	0.1641	0.4769	-9.2555	50.972	11.0281
22	2.6985	-0.1238	0.2725	2.9819	-2.5565	5.9	-0.0759	0.2849	0.6025	-0.205	-0.0138	-0.0027	0.1063	0.347	0.076	0.5928	-0.0439	-0.1032	0.4223	0.054	0.5138	2.4383	55.4005	19.1945
23	3.9225	-3.3756	4.2269	3.1455	-4.0998	5.3207	-0.6611	0.209	0.877	0.3149	0.5177	0.3435	-1.4019	-0.5565	0.3224	0.8486	-0.1884	-0.2437	0.7668	0.3389	0.7842	-9.8927	64.1275	6.2062
24	2.689	2.1162	2.513	2.1736	1.1345	2.9976	0.1209	0.3958	-0.9155	0.2638	-0.047	-0.36	0.7984	0.7946	-0.8792	0.8016	-0.0443	-0.269	0.6973	-0.076	0.3702	-16.9736	-14.4586	12.9981
25	1.8581	1.6712	1.0842	3.5813	0.7224	2.7457	-0.2114	0.3919	0.2337	-0.4605	0.2835	-0.0937	0.3116	0.0373	-0.2726	0.5648	-0.0344	-0.0908	0.6201	-0.1749	0.3233	-14.7281	-4.4705	8.1878
26	3.1201	0.9059	1.088	1.7163	1.0034	2.0648	-0.1756	-0.0312	1.0225	0.1775	-0.552	0.6602	0.2985	-0.4593	0.283	0.5873	-0.1599	-0.138	0.7421	-0.0331	0.3836	-24.8037	-8.7282	21.3451
27	3.0783	2.4685	0.4121	3.8865	0.3817	2.9866	0.4776	0.6648	0.4628	0.8465	-0.2345	0.8945	0.008	-0.8734	0.0851	0.5158	-0.022	-0.1908	0.9228	-0.1244	0.7225	-34.5584	-7.704	22.4954
28	8.2077	2.5294	0.5791	5.4685	2.4259	5.466	-1.3338	0.3057	0.1445	-0.8846	0.9975	1.0443	-0.6286	-1.5007	0.4331	1.0546	-0.0348	0.0131	0.6486	-0.0478	0.3255	-29.1453	-12.6255	34.2536
29	4.3984	0.7301	0.9626	5.1217	2.0382	6.5178	0.1962	0.169	0.5786	0.6932	0.1021	-0.857	-0.8393	-0.1288	-0.6823	0.8207	0.0246	-0.114	0.3139	-0.0098	0.5724	-13.0457	-8.7689	42.8187
30	0.1169	-0.1911	-0.2029	0.6512	0.8611	1.4045	0.6802	0.1629	-0.3268	1.2263	0.4196	0.5285	2.0625	-0.7177	-0.7179	0.8856	-0.2787	-0.3503	0.7141	-0.0559	0.5226	-29.4121	-20.7537	21.5951

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 57 through 97 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 98 through 121 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 122 through 164 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 165 through 198 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 57 through 121 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 122 through 150 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 151 through 193 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 57 through 97 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 98 through 121 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 122 through 150 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 151 through 164 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 165 through 194 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 57 through 87 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 88 through 121 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 122 through 150 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 151 through 193 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 57 through 87 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 88 through 121 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 122 through 152 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 153 through 193 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 58 through 121 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 122 through 164 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 165 through 193 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 57 through 121 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 122 through 195 )
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 57 through 97 )
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 98 through 123 )
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 124 through 148 )
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 149 through 164 )
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 165 through 191 )

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi