PDB-6f9g: Ligand binding domain of P. putida KT2440 polyamine chemorecpetor...

ID or keywords:

Entry

Database: PDB / ID: 6f9g

Title

Ligand binding domain of P. putida KT2440 polyamine chemorecpetors McpU in complex putrescine.

Components

Methyl-accepting chemotaxis protein McpU

Keywords

SIGNALING PROTEIN / Ligand binding domain / CHEMOTACTIC TRANSDUCER

Function / homology

Function and homology information

chemotaxis / signal transduction / plasma membrane
Similarity search - Function

Biological species

Pseudomonas putida KT2440 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.388 Å

Authors

Gavira, J.A. / Conejero-Muriel, M.T. / Ortega, A. / Martin-Mora, D. / Corral-Lugo, A. / Morel, B. / Krell, T.

Funding support

Spain, 1items

Citation

Journal: J. Mol. Biol. / Year: 2018
Title: Structural Basis for Polyamine Binding at the dCACHE Domain of the McpU Chemoreceptor from Pseudomonas putida.
Authors: Gavira, J.A. / Ortega, A. / Martin-Mora, D. / Conejero-Muriel, M.T. / Corral-Lugo, A. / Morel, B. / Matilla, M.A. / Krell, T.

History

Deposition	Dec 14, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 23, 2018	Group: Data collection / Database references / Source and taxonomy Category: citation / citation_author / entity_src_gen 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 / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_vector_type
Revision 1.2	Jun 13, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6f9g.cif.gz	544.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6f9g_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	6f9g_full_validation.pdf.gz	1.5 MB	Display
Data in XML	6f9g_validation.xml.gz	50.8 KB	Display
Data in CIF	6f9g_validation.cif.gz	69.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f9/6f9g ftp://data.pdbj.org/pub/pdb/validation_reports/f9/6f9g	HTTPS FTP

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Related structure data

Similar structure data	5zt8-2 3m19-1 4ekx-3 5j7c-1 3m19-2 3ht1-1 4q3i-1 2q1e-2 2f37-2 4qrm-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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 protein McpU

B: Methyl-accepting chemotaxis protein McpU

C: Methyl-accepting chemotaxis protein McpU

D: Methyl-accepting chemotaxis protein McpU

E: Methyl-accepting chemotaxis protein McpU

hetero molecules

175 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Methyl-accepting chemotaxis protein McpU

hetero molecules

defined by author
34.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Methyl-accepting chemotaxis protein McpU

hetero molecules

defined by author
34.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Methyl-accepting chemotaxis protein McpU

hetero molecules

defined by author
34.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Methyl-accepting chemotaxis protein McpU

hetero molecules

defined by author
35.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Methyl-accepting chemotaxis protein McpU

hetero molecules

defined by author
35 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	133.984, 164.521, 123.612
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Methyl-accepting chemotaxis protein McpU Mass: 34732.844 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: Recombinant protein has the N-terminal extension MGSSHHHHHHSGLVPRGSHM containing the hexa-histidine tag. Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: mcpU, PP_1228 / Plasmid: PET28B PLUS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q88NI1
#2: Chemical	ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE Mass: 88.151 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₂N₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.02 Å³/Da / Density % sol: 39.2 %
Crystal grow	Temperature: 293 K / Method: liquid diffusion / pH: 6 Details: 30% PEG 4K, 0.2M NH4-acetate, 0.1M Na-acetate pH 6.0 PH range: 5.0-9.0

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.9790, 0.979117,0.9767

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2017 / Details: Toroidal mirror

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.979	1
2	0.979117	1
3	0.9767	1

Reflection

Resolution: 2.388→79.53 Å / Num. obs: 52459 / % possible obs: 96.31 % / Redundancy: 3 % / CC_1/2: 0.995 / R_merge(I) obs: 0.09447 / R_pim(I) all: 0.06157 / R_rim(I) all: 0.1136 / Net I/σ(I): 8.8

Reflection shell

Resolution: 2.388→2.473 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.5978 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 4922 / CC_1/2: 0.726 / R_pim(I) all: 0.4033 / R_rim(I) all: 0.7273 / % possible all: 90.98

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
Aimless		data scaling
Auto-Rickshaw		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.388→79.53 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.94

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2345	2510	4.79 %	Random
R_work	0.1947	-	-	-
obs	0.1967	52441	96.23 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 49.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.388→79.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9942	0	68	297	10307

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	10993
X-RAY DIFFRACTION	f_angle_d	0.551	14997
X-RAY DIFFRACTION	f_dihedral_angle_d	9.258	8848
X-RAY DIFFRACTION	f_chiral_restr	0.04	1619
X-RAY DIFFRACTION	f_plane_restr	0.003	2061

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 (%)
2.3868-2.4327	0.3516	134	0.3113	2430	X-RAY DIFFRACTION	86
2.4327-2.4823	0.3348	146	0.2853	2718	X-RAY DIFFRACTION	96
2.4823-2.5363	0.3556	164	0.2702	2812	X-RAY DIFFRACTION	99
2.5363-2.5953	0.2711	133	0.2588	2823	X-RAY DIFFRACTION	99
2.5953-2.6602	0.2998	134	0.2497	2834	X-RAY DIFFRACTION	99
2.6602-2.7321	0.2954	115	0.2363	2858	X-RAY DIFFRACTION	99
2.7321-2.8125	0.299	150	0.2415	2825	X-RAY DIFFRACTION	98
2.8125-2.9033	0.2477	136	0.2348	2775	X-RAY DIFFRACTION	98
2.9033-3.0071	0.2792	127	0.2284	2761	X-RAY DIFFRACTION	96
3.0071-3.1275	0.2819	128	0.2194	2816	X-RAY DIFFRACTION	97
3.1275-3.2698	0.2702	152	0.2003	2813	X-RAY DIFFRACTION	99
3.2698-3.4422	0.2195	146	0.1901	2824	X-RAY DIFFRACTION	98
3.4422-3.6579	0.2211	157	0.174	2779	X-RAY DIFFRACTION	97
3.6579-3.9403	0.2079	135	0.1666	2717	X-RAY DIFFRACTION	94
3.9403-4.3368	0.2077	120	0.1555	2802	X-RAY DIFFRACTION	96
4.3368-4.9643	0.1791	160	0.1406	2791	X-RAY DIFFRACTION	96
4.9643-6.2541	0.2111	135	0.1845	2774	X-RAY DIFFRACTION	94
6.2541-79.5759	0.1856	138	0.1803	2779	X-RAY DIFFRACTION	91

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	7.8439	-1.8467	3.9872	2.4763	-0.0949	3.3628	0.2115	-0.6542	0.1707	0.3035	-0.0516	-0.4354	0.512	-0.2807	-0.0885	0.2962	-0.0173	-0.0353	0.2738	0.0395	0.3088	52.9489	61.0396	57.9304
2	2.2756	0.4138	0.216	3.0182	1.2914	4.0609	-0.0109	0.2001	0.1909	-0.4009	-0.015	0.1967	-0.3062	-0.135	0.0157	0.269	0.0296	0.0172	0.239	0.0528	0.2453	40.6663	73.5376	38.9821
3	2.6732	-0.2828	0.8876	3.7962	0.7569	2.9642	0.0999	0.4593	-0.0426	-0.1784	0.0294	-0.4556	0.0778	0.4482	-0.1623	0.3094	0.0175	0.0759	0.3625	-0.0092	0.2561	54.9988	66.065	39.0702
4	4.622	-0.2497	2.3253	2.8451	0.7047	2.5111	-0.2807	-0.4601	0.3139	0.4423	0.1566	-0.7511	-0.37	-0.0699	-0.0381	0.3322	-0.0155	-0.1263	0.2629	-0.011	0.4734	61.2694	68.7777	56.9738
5	0.8421	-1.566	0.3978	2.436	-0.3192	4.5587	-0.0753	0.2153	0.0597	0.0322	0.1267	-1.3072	-0.2261	0.7351	-0.0813	0.3461	0.0172	-0.0811	0.3899	-0.0168	0.7132	70.8659	63.3865	55.5797
6	4.8388	0.4909	2.4201	1.7467	1.1858	3.3104	-0.0461	0.0343	0.0146	0.2065	0.2399	-0.2989	-0.0393	0.4796	-0.1474	0.2665	0.0105	0.0087	0.3143	-0.0055	0.249	48.3336	71.2541	66.693
7	4.5504	-0.7532	-1.1341	2.1161	-0.0789	3.4885	0.2402	0.475	-0.1154	-0.0576	-0.2107	0.252	0.4545	0.0915	0.0871	0.1642	-0.0296	0.0323	0.1591	-0.0052	0.2377	30.935	59.4947	57.1658
8	4.8092	0.0197	-1.3752	4.2229	0.0807	3.6569	-0.2852	0.3379	-0.0198	-0.3287	0.1122	0.2249	0.2861	-0.754	0.0037	0.3802	-0.0796	-0.0294	0.3617	-0.0259	0.3744	15.7944	60.3081	58.5327
9	0.969	-0.4642	0.0792	1.5933	-0.2739	2.3819	-0.0207	-0.2432	-0.1503	0.3437	0.0446	0.1001	-0.0735	-0.0431	0.0788	0.2903	-0.0115	0.0902	0.2879	0.0101	0.2754	26.9972	60.4562	70.4871
10	2.3749	-0.5244	0.4591	3.0557	0.0481	1.995	0.0139	-0.1438	-0.1759	0.3877	0.0457	-0.0875	-0.0628	0.1272	-0.0141	0.3454	-0.002	0.0288	0.2687	0.0122	0.2171	37.7189	64.261	71.1693
11	2.9448	-0.1051	1.3743	2.0118	-0.0159	2.2033	-0.2332	0.1664	-0.3717	0.7158	0.5034	-1.6948	0.8613	0.7565	-0.1507	0.7042	0.1001	-0.2456	0.6148	-0.126	1.0144	61.3128	63.7703	78.9494
12	5.1755	-0.7099	-1.853	3.1039	-0.2377	2.558	0.2102	-0.9439	-0.4631	0.8123	-0.0991	-0.344	0.5173	0.1587	0.0569	0.8292	-0.0584	-0.1567	0.4379	0.0559	0.4913	48.0881	61.9543	83.5419
13	2.0111	0.2709	-1.3185	0.1463	-0.3724	1.3798	0.1062	-1.351	0.2042	0.8437	-0.2039	-0.1988	0.1833	0.4689	-0.1193	1.1641	-0.0722	-0.2396	0.8719	-0.0101	0.5405	52.6693	67.2269	89.57
14	2.8998	2.6695	0.0189	2.6891	1.0705	3.439	0.3193	0.0298	0.0485	0.5687	-0.012	-0.4621	0.3893	0.402	-0.2444	0.5047	0.0978	-0.0789	0.3545	-0.0554	0.4151	52.0814	72.8858	77.9022
15	1.9067	0.8858	-1.3782	1.1449	-2.0484	6.8532	0.0307	-0.055	-0.0514	0.106	0.0921	0.0632	0.316	-0.6199	-0.1692	0.2982	-0.0421	0.0175	0.3095	0.0092	0.2918	54.6557	28.0352	62.9901
16	4.1476	-1.0005	-0.7862	4.0197	0.1632	4.6524	0.0781	0.5409	0.1083	-0.6595	-0.1534	-0.1391	-0.1318	-0.0588	0.0904	0.311	-0.028	0.0134	0.2382	0.0247	0.2904	67.3872	39.5898	43.6644
17	1.2233	-0.8231	1.3291	0.9595	-0.7442	1.9583	-0.0294	-0.0733	0.0812	0.1779	0.0889	-0.1931	0.0245	0.2297	-0.0637	0.2612	0.0095	-0.0129	0.2788	0.0392	0.3896	73.4338	39.4653	55.2752
18	2.0865	-0.6292	-0.5729	2.0377	0.2777	3.7186	-0.0413	-0.0724	0.072	0.2991	-0.0206	-0.1136	0.0231	-0.0788	0.0735	0.2911	-0.0213	-0.0651	0.2226	0.013	0.2774	65.2282	34.7767	62.5257
19	3.4569	-0.2909	-0.8531	2.6076	-0.1563	4.3808	0.1995	-0.5792	0.2354	0.896	-0.0074	0.0493	-0.5242	0.1562	-0.152	0.6256	-0.037	0.0121	0.4296	-0.0589	0.3263	61.6788	34.5545	82.5736
20	6.3025	-0.3746	-3.8003	3.3987	1.5575	8.686	-0.2101	-0.5399	-0.1608	0.5453	0.074	0.07	0.2553	0.1077	0.1802	0.4247	-0.0009	-0.004	0.2781	0.0135	0.2587	58.6136	26.2573	77.9602
21	2.5633	-0.9425	-2.1384	2.5012	1.3464	2.6061	-0.2403	-0.6835	-0.0371	0.3605	0.1327	0.1697	-0.0229	1.1126	0.0125	0.2623	-0.0094	0.0024	0.3395	-0.0159	0.3291	44.7292	37.9484	60.6765
22	4.201	0.1708	0.2924	3.6186	0.161	3.7564	-0.126	0.1508	-0.173	-0.0947	-0.0304	-0.0123	-0.0204	0.524	0.1171	0.2552	-0.0174	-0.0264	0.264	-0.0358	0.2389	48.2395	25.8468	43.0008
23	2.5541	-0.0599	-0.501	1.5654	0.0555	1.2996	-0.0746	0.3073	0.234	-0.2777	0.0613	0.1563	-0.0659	-0.1966	0.0316	0.4042	-0.0051	-0.095	0.3111	0.0162	0.2789	36.4805	27.4813	39.288
24	2.5829	-0.5098	-0.8576	2.7425	0.0803	3.7443	0.3186	-0.0034	0.0343	0.3275	-0.167	0.4635	-0.2975	-0.0973	-0.0744	0.2717	0.0362	-0.051	0.2449	-0.0381	0.3464	35.0768	31.3459	49.0741
25	1.6012	-0.7718	-0.8041	1.7467	0.5352	3.4988	-0.3078	-0.3568	-0.2584	0.7541	0.0821	0.3433	0.228	-0.2745	-0.0085	0.5722	0.0091	0.1042	0.3087	0.0197	0.4441	32.8507	30.8315	66.8438
26	3.0089	-1.0591	-0.2872	3.537	0.0464	5.2445	0.0431	-0.116	0.1075	0.5306	0.2194	0.2065	-0.6967	-0.2654	-0.0222	0.3444	0.0655	0.0884	0.2492	-0.0227	0.3842	33.7557	39.5911	69.6313
27	2.1472	1.3152	-0.0182	2.0554	-0.6582	0.7308	0.0986	0.5351	-0.2123	0.0325	-0.0411	0.0608	0.1087	-0.1537	-0.0623	0.2826	-0.0356	-0.0168	0.2765	-0.0568	0.2488	50.0725	-4.9471	66.8592
28	1.5174	-0.3547	-0.8844	2.3234	-0.1697	3.2218	0.0307	-0.38	-0.0719	0.5377	-0.1135	-0.6748	-0.1128	0.286	0.0577	0.4383	-0.1017	-0.174	0.3572	0.103	0.4249	68.2414	5.934	77.9432
29	3.6411	0.8075	-0.3773	3.0624	-0.6719	0.5448	0.0859	-0.1794	-0.0865	0.323	-0.0956	0.2151	-0.1079	-0.0289	0.0033	0.4576	-0.0416	0.0313	0.2801	-0.0006	0.2547	46.7966	1.4771	77.7755
30	3.671	0.6063	0.7547	2.349	-0.6006	3.3143	0.2364	0.1056	0.0959	0.1999	-0.1803	0.5656	0.1027	-0.212	-0.002	0.4027	-0.0638	0.0582	0.2481	-0.0693	0.3771	38.0624	-6.4481	74.8295

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 53 through 93 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 94 through 171 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 172 through 224 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 225 through 260 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 261 through 313 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 53 through 92 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 93 through 123 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 124 through 141 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 142 through 193 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 194 through 248 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 249 through 260 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 261 through 275 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 276 through 290 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 291 through 313 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 54 through 93 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 94 through 141 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 142 through 192 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 193 through 249 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 250 through 288 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 289 through 313 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 52 through 93 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 94 through 123 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 124 through 193 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 194 through 224 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 225 through 288 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 289 through 313 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 53 through 93 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 94 through 193 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 194 through 288 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 289 through 313 )

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