PDB-8py1: Sensor domain of Asticcacaulis benevestitus chemoreceptor in comp...

ID or keywords:

Entry

Database: PDB / ID: 8py1

Title

Sensor domain of Asticcacaulis benevestitus chemoreceptor in complex with formate.

Components

Methyl-accepting chemotaxis protein

Keywords

SIGNALING PROTEIN / chemotaxis / chemoreceptor / Asticcacaulis benevestitus

Function / homology

Function and homology information

signal transduction / plasma membrane
Similarity search - Function

Biological species

Asticcacaulis benevestitus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Gavira, J.A. / Krell, T. / Monteagudo-Cascales, E. / Velando, F. / Matilla, M.A. / Martinez-Rodriguez, S.

Funding support

Spain, 2items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Bacterial sensor evolved by decreasing complexity.
Authors: Monteagudo-Cascales, E. / Gavira, J.A. / Xing, J. / Velando, F. / Matilla, M.A. / Zhulin, I.B. / Krell, T.

History

Deposition	Jul 24, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8py1.cif.gz	196.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8py1.ent.gz	157.1 KB	Display	PDB format
PDBx/mmJSON format	8py1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8py1_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8py1_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8py1_validation.xml.gz	22.2 KB	Display
Data in CIF	8py1_validation.cif.gz	28.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/py/8py1 ftp://data.pdbj.org/pub/pdb/validation_reports/py/8py1	HTTPS FTP

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Related structure data

Related structure data	8py0C C: citing same article (ref.)
Similar structure data	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	#167 - Nov 2013 SNARE Proteins similarity (2) #158 - Feb 2013 Proton-Gated Urea Channel similarity (8) #190 - Oct 2015 Two-component Systems similarity (5)

Deposited unit

A: Methyl-accepting chemotaxis protein

B: Methyl-accepting chemotaxis protein

C: Methyl-accepting chemotaxis protein

hetero molecules

59.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Methyl-accepting chemotaxis protein

hetero molecules

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

2

B: Methyl-accepting chemotaxis protein

hetero molecules

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

3

C: Methyl-accepting chemotaxis protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	103.768, 103.768, 220.404
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

#1: Protein	Methyl-accepting chemotaxis protein Mass: 19830.166 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Asticcacaulis benevestitus (bacteria) / Gene: ABENE_03230 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V4PJJ2
#2: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.82 %
Crystal grow	Temperature: 293 K / Method: batch mode / pH: 8.5 Details: 0.1 M Tris hydrochloride pH 8.5, 2.0 M Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 15, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.1→73.38 Å / Num. obs: 35374 / % possible obs: 99.04 % / Redundancy: 8 % / CC_1/2: 0.997 / R_merge(I) obs: 0.1162 / R_pim(I) all: 0.0378 / R_rim(I) all: 0.1225 / Χ²: 0.83 / Net I/σ(I): 4.3
Reflection shell	Resolution: 2.1→2.175 Å / Redundancy: 5.4 % / R_merge(I) obs: 1.179 / Num. unique obs: 3397 / CC_1/2: 0.701 / R_pim(I) all: 0.5567 / R_rim(I) all: 1.311 / Χ²: 0.42

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→73.38 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3059	1779	5.06 %
R_work	0.2655	-	-
obs	0.2674	35178	99.01 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.1→73.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3506	0	19	105	3630

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002
X-RAY DIFFRACTION	f_angle_d	0.531
X-RAY DIFFRACTION	f_dihedral_angle_d	5.229	518
X-RAY DIFFRACTION	f_chiral_restr	0.043	588
X-RAY DIFFRACTION	f_plane_restr	0.006	650

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 (%)
2.1-2.16	0.3958	146	0.3895	2439	X-RAY DIFFRACTION	96
2.16-2.22	0.3938	134	0.3409	2523	X-RAY DIFFRACTION	99
2.22-2.29	0.359	111	0.3543	2482	X-RAY DIFFRACTION	97
2.29-2.37	0.3282	157	0.2908	2522	X-RAY DIFFRACTION	100
2.37-2.47	0.3413	134	0.2787	2559	X-RAY DIFFRACTION	99
2.47-2.58	0.3885	140	0.2759	2546	X-RAY DIFFRACTION	100
2.58-2.72	0.2848	138	0.2739	2556	X-RAY DIFFRACTION	100
2.72-2.89	0.3287	119	0.2858	2580	X-RAY DIFFRACTION	99
2.89-3.11	0.3507	149	0.2647	2553	X-RAY DIFFRACTION	99
3.11-3.42	0.3279	148	0.2631	2580	X-RAY DIFFRACTION	99
3.42-3.92	0.2642	122	0.2403	2626	X-RAY DIFFRACTION	100
3.92-4.94	0.2707	133	0.2266	2665	X-RAY DIFFRACTION	100
4.94-73.38	0.2641	148	0.2573	2768	X-RAY DIFFRACTION	100

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	1.4598	1.452	0.5783	1.5195	0.3259	1.1969	0.0152	-0.2922	-0.36	0.3424	0.0964	-0.0854	0.5982	0.0941	0.0005	0.4036	0.0342	-0.0515	0.3009	-0.0191	0.2851	-17.602	9.9124	-3.411
2	1.1527	0.6884	-0.2834	0.607	0.2793	0.6208	-0.3359	-0.7173	-0.0251	0.9128	0.3438	0.1568	0.1541	-0.8155	-0.0017	0.4322	0.0277	0.0283	0.4063	-0.0558	0.3626	-28.952	10.2987	-0.0255
3	0.2945	-0.2667	0.1918	0.2386	-0.2589	0.2269	-0.1725	0.1133	1.1194	-0.1163	0.5059	0.9499	-0.2985	-0.6072	0.003	0.6392	0.0024	0.0265	0.5186	-0.0155	0.4824	-29.3449	20.5051	-14.0319
4	0.1472	-0.0024	0.1375	0.2953	-0.1311	0.3063	-0.2233	-0.188	0.5543	0.5421	0.2427	-0.1239	-0.4025	0.6316	-0.0028	0.3341	0.0419	0.0199	0.2902	-0.0671	0.3013	-16.2133	20.2345	-7.8607
5	0.5705	0.4435	-0.7585	0.548	-0.6413	0.8468	-0.0695	0.2759	-0.0322	-0.1684	0.1181	0.1416	0.1329	-0.0354	-0	0.2939	0.0035	-0.0266	0.341	-0.0296	0.2653	-25.6581	11.6268	-18.3977
6	0.4391	-0.2505	-0.3395	0.5728	0.1865	0.3375	-0.0251	0.5409	0.0284	-0.2968	0.2271	-0.6461	0.141	0.1667	0	0.2982	-0.0218	-0.0032	0.3787	-0.01	0.3135	-18.898	13.008	-23.0998
7	0.4115	0.1022	-0.1681	0.0641	-0.0872	0.3128	0.3255	-0.675	-0.7389	-0.0496	-0.2856	-0.2558	0.5354	0.1177	-0.0073	0.4418	-0.0727	-0.1018	0.2873	0.004	0.3764	-27.1803	-0.5125	-14.2983
8	0.8628	0.1687	0.266	0.0564	-0.0104	0.9914	-0.2591	0.5098	-0.843	0.183	-0.1807	-0.938	0.9477	0.7742	-0.0264	0.4419	0.0757	-0.0314	0.293	-0.0565	0.3886	-15.4293	2.4229	-16.861
9	0.1661	0.0448	0.3852	1.5496	0.091	1.0261	-0.1132	0.0286	-0.3413	0.1878	0.0126	0.1417	0.5308	-0.1794	0.001	0.3294	-0.0285	-0.0303	0.3147	0.0021	0.3412	-25.6791	6.2431	-11.7715
10	0.4646	0.3982	-0.2946	2.2673	-0.1868	0.6411	0.0782	0.37	-0.3381	0.2636	0.0215	-0.5013	0.6338	0.3346	0.0136	0.4107	0.1683	-0.0943	0.4258	-0.0685	0.3615	-11.0311	7.6752	-12.9628
11	1.5081	0.5405	0.7838	0.8116	0.2816	1.638	0.0441	-0.6795	1.0034	-0.1794	-0.0288	-0.0316	-0.6936	-0.8011	-0.0261	0.4287	-0.0373	0.1533	0.4151	-0.0543	0.7058	-57.5055	24.6811	-16.641
12	0.6821	0.3903	-0.4209	0.63	0.2968	0.5017	-0.1988	0.105	0.0632	-0.0008	0.0315	-0.387	-0.0254	0.0281	-0.0005	0.3729	-0.0114	0.0703	0.5907	0.0099	0.5579	-49.7934	21.2418	-14.4151
13	2.7698	1.3525	0.1472	2.0106	-0.331	1.3136	0.0657	0.0691	0.0574	-0.0397	-0.0535	0.1363	0.1121	-0.1989	-0	0.2496	-0.0186	0.043	0.357	0.0083	0.3492	-55.8029	11.3447	-17.911
14	0.1322	-0.0236	-0.0722	0.9502	-0.2228	0.4018	-0.42	0.0471	0.0113	0.0466	0.2768	0.2868	-0.0213	-0.1658	-0.0004	0.3621	-0.0538	0.0409	0.4576	0.0147	0.5154	-65.9294	14.6076	-19.636
15	0.8598	0.0516	-0.3755	0.4096	0.278	0.4062	0.5011	-0.1896	0.0998	0.3244	0.3565	0.1642	-0.1296	0.5641	0.0033	0.7166	-0.0854	0.1354	0.8709	-0.1552	0.6108	-69.0847	14.3433	22.0202
16	0.0853	0.049	-0.0132	0.1036	0.0788	0.048	0.5424	0.2481	0.4772	-0.4174	-0.145	-0.0715	0.221	-0.1528	0.0024	0.7302	0.0179	0.2108	0.8354	0.0178	0.9422	-77.2383	16.5281	9.1319
17	0.5789	-0.4207	-0.0204	0.4064	0.0244	0.2499	-0.091	-0.0583	0.4179	-0.1871	0.4116	0.1331	-0.0726	0.6561	0.0011	0.6211	-0.1628	0.1698	0.9782	-0.1829	0.6221	-68.4344	16.6667	11.7277
18	0.0755	-0.1108	0.213	0.5677	-0.8592	1.23	0.3626	-0.3761	0.5045	-0.0174	0.1776	-0.2052	0.7399	1.3657	0.0862	0.6633	0.1828	0.0436	1.1859	-0.2866	0.5807	-61.2957	7.6445	7.7087
19	0.1079	-0.0495	0.087	0.5664	-0.5	0.4275	0.1444	-1.0746	-0.0335	-0.5632	-0.1896	0.014	0.4032	1.3066	-0.0184	0.6331	0.0886	0.0575	1.5749	-0.1485	0.6742	-52.5256	10.1168	10.4036
20	0.0739	0.0162	0.0085	0.4507	-0.3042	0.2112	0.3852	0.0539	-0.8784	0.0081	0.005	-0.6116	0.7736	1.1411	0.0011	0.7823	0.3007	-0.0458	1.0882	-0.1542	0.7014	-63.7416	0.7057	16.5175
21	0.4678	0.309	-0.556	1.5447	-0.9731	0.8001	0.1534	-0.1799	0.1577	0.0031	0.1635	-0.2357	0.322	0.7385	0.0001	0.5457	0.1255	-0.0487	0.9845	-0.207	0.6266	-65.256	7.4293	15.4155

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 40 through 62 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 63 through 80 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 81 through 90 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 91 through 100 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 101 through 121 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 122 through 140 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 141 through 151 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 152 through 160 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 161 through 176 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 177 through 195 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 39 through 70 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 71 through 90 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 91 through 176 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 177 through 194 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 39 through 62 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 63 through 70 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 71 through 100 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 101 through 121 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 122 through 140 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 141 through 160 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 161 through 190 )

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