PDB-7psg: Structure of the ligand binding domain of the PacA (ECA2226) chem...

ID or keywords:

Entry

Database: PDB / ID: 7psg

Title

Structure of the ligand binding domain of the PacA (ECA2226) chemoreceptor of Pectobacterium atrosepticum SCRI1043 in complex with betaine.

Components

Methyl-accepting chemotaxis protein

Keywords

SIGNALING PROTEIN / Ligand binding domain / Pectobacterium atrosepticum / chemotactic transducer

Function / homology

Function and homology information

chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane
Similarity search - Function

Biological species

Pectobacterium atrosepticum SCRI1043 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.91 Å

Authors

Gavira, J.A. / Matilla, M.A. / Velando, F. / Krell, T.

Funding support

Spain, 2items

Citation

Journal: Mbio / Year: 2022
Title: Chemotaxis of the Human Pathogen Pseudomonas aeruginosa to the Neurotransmitter Acetylcholine.
Authors: Matilla, M.A. / Velando, F. / Tajuelo, A. / Martin-Mora, D. / Xu, W. / Sourjik, V. / Gavira, J.A. / Krell, T.

History

Deposition	Sep 23, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 11, 2022	Provider: repository / Type: Initial release
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1	May 1, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7psg.cif.gz	746.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7psg.ent.gz	523.6 KB	Display	PDB format
PDBx/mmJSON format	7psg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7psg_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	7psg_full_validation.pdf.gz	1.3 MB	Display
Data in XML	7psg_validation.xml.gz	43.4 KB	Display
Data in CIF	7psg_validation.cif.gz	61.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ps/7psg ftp://data.pdbj.org/pub/pdb/validation_reports/ps/7psg	HTTPS FTP

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Related structure data

Related structure data	7prqC 7prrC 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	#158 - Feb 2013 Proton-Gated Urea Channel similarity (4)

Deposited unit

A: Methyl-accepting chemotaxis protein

B: Methyl-accepting chemotaxis protein

C: Methyl-accepting chemotaxis protein

D: Methyl-accepting chemotaxis protein

hetero molecules

134 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Methyl-accepting chemotaxis protein

B: Methyl-accepting chemotaxis protein

hetero molecules

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

2

C: Methyl-accepting chemotaxis protein

D: Methyl-accepting chemotaxis protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.776, 83.437, 94.912
Angle α, β, γ (deg.)	90.000, 106.861, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

#1: Protein	Methyl-accepting chemotaxis protein Mass: 33223.051 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium atrosepticum SCRI1043 (bacteria) Strain: SCRI 1043 / ATCC BAA-672 / Gene: ECA2226 / Plasmid: PET28B+ Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q6D515
#2: Chemical	ChemComp-BET / TRIMETHYL GLYCINE Mass: 118.154 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₁₂NO₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.3 Å³/Da / Density % sol: 46.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium acetate trihydrate, 0.1 M Tris hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: MASSIF-3 / Wavelength: 0.9677 Å

Detector

Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 12, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.9677 Å / Relative weight: 1

Reflection

Resolution: 1.91→61.45 Å / Num. obs: 91911 / % possible obs: 98.3 % / Redundancy: 2.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.059 / R_pim(I) all: 0.041 / R_rim(I) all: 0.072 / Net I/σ(I): 9.8 / Num. measured all: 270640 / Scaling rejects: 316

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.91-1.94	3.1	1.309	14089	4596	0.462	0.895	1.591	0.9	99.5
10.46-61.45	2.6	0.026	1505	573	0.992	0.02	0.033	31.2	95

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Processing

Software

Name	Version	Classification
PHENIX	1.19-4092	refinement
XDS		data reduction
Aimless		data scaling
PDB_EXTRACT	3.27	data extraction
MR-Rosetta		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: RoseTTAFold

Resolution: 1.91→39.99 Å / SU ML: 0.2536 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8428
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2267	4616	5.03 %
R_work	0.1851	87117	-
obs	0.1873	91733	98.02 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 53.94 Å²

Refinement step

Cycle: LAST / Resolution: 1.91→39.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8324	0	56	395	8775

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0106	8710
X-RAY DIFFRACTION	f_angle_d	1.2769	11900
X-RAY DIFFRACTION	f_chiral_restr	0.0724	1299
X-RAY DIFFRACTION	f_plane_restr	0.0111	1556
X-RAY DIFFRACTION	f_dihedral_angle_d	7.2239	1218

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 (%)
1.91-1.93	0.3804	158	0.3779	2911	X-RAY DIFFRACTION	98.27
1.93-1.95	0.3903	153	0.3517	2919	X-RAY DIFFRACTION	99.13
1.95-1.98	0.3366	158	0.3295	2943	X-RAY DIFFRACTION	98.85
1.98-2	0.3098	134	0.3162	2900	X-RAY DIFFRACTION	99.31
2-2.03	0.3462	177	0.3055	2905	X-RAY DIFFRACTION	99.07
2.03-2.06	0.3495	163	0.2934	2885	X-RAY DIFFRACTION	99.22
2.06-2.09	0.3631	143	0.289	2946	X-RAY DIFFRACTION	99.23
2.09-2.12	0.3414	149	0.2813	2937	X-RAY DIFFRACTION	99.13
2.12-2.15	0.2798	172	0.2595	2920	X-RAY DIFFRACTION	99.07
2.15-2.19	0.3008	136	0.2309	2932	X-RAY DIFFRACTION	98.9
2.19-2.22	0.2641	160	0.2282	2900	X-RAY DIFFRACTION	99.03
2.22-2.26	0.2287	151	0.2159	2929	X-RAY DIFFRACTION	98.72
2.26-2.31	0.2584	160	0.2122	2921	X-RAY DIFFRACTION	98.85
2.31-2.36	0.2995	153	0.2128	2892	X-RAY DIFFRACTION	98.58
2.36-2.41	0.2801	157	0.2015	2905	X-RAY DIFFRACTION	98.49
2.41-2.46	0.2486	130	0.2023	2957	X-RAY DIFFRACTION	98.19
2.46-2.52	0.221	152	0.2061	2934	X-RAY DIFFRACTION	98.31
2.52-2.59	0.2809	132	0.2143	2869	X-RAY DIFFRACTION	97.82
2.59-2.67	0.2544	156	0.2014	2867	X-RAY DIFFRACTION	97.71
2.67-2.75	0.2269	164	0.1891	2893	X-RAY DIFFRACTION	97.76
2.75-2.85	0.2593	167	0.192	2884	X-RAY DIFFRACTION	97.98
2.85-2.97	0.2561	155	0.197	2866	X-RAY DIFFRACTION	96.36
2.97-3.1	0.2363	142	0.1949	2813	X-RAY DIFFRACTION	94.53
3.1-3.27	0.2425	156	0.1942	2686	X-RAY DIFFRACTION	91.32
3.27-3.47	0.213	154	0.1797	2933	X-RAY DIFFRACTION	98.85
3.47-3.74	0.2286	169	0.1668	2931	X-RAY DIFFRACTION	98.63
3.74-4.11	0.1939	158	0.1508	2918	X-RAY DIFFRACTION	97.99
4.11-4.71	0.1774	147	0.1335	2928	X-RAY DIFFRACTION	97.5
4.71-5.93	0.1506	158	0.1406	2916	X-RAY DIFFRACTION	97.31
5.93-39.99	0.1977	152	0.1665	2977	X-RAY DIFFRACTION	96.93

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	2.74174820969	-3.89178692626	2.08953948627	9.326789303	-3.72540010421	3.6485998126	-0.147866306599	0.0121000248528	0.202122814607	-0.00923922906746	0.152692569594	-0.169125670142	-0.277319281811	-0.0325284567375	-0.019548470954	0.381601398207	-0.0540684166295	0.00814474433963	0.35409039293	0.00509019751788	0.241720371239	-15.4243028358	-8.55083310601	-26.5311006706
2	4.68215215381	-1.40757426532	0.533352066448	3.78418254424	-0.247438888813	3.2716250498	0.0464289597201	0.11471683993	-0.670068177185	0.0426236112628	-0.0448386154545	0.342124389933	0.597681039657	-0.237297250864	0.0290584184609	0.419049565204	-0.100741426325	-0.00116235930316	0.297528811673	-0.0255300832767	0.318444823398	-18.0675889992	-34.9684695164	-26.5422357562
3	1.26926436607	-1.39089822617	-0.215182509962	3.43674338313	0.0626164376574	0.847405834028	0.0476255234231	0.245278501837	-0.0198474878946	-0.232417041261	-0.127543423039	0.128570599769	0.00316007232904	-0.00987701260569	0.0823268314729	0.355017846886	-0.0480273597314	-0.0170908725349	0.402668844756	0.0221377937887	0.270518796868	-18.9793299238	-18.2104087814	-35.7057017757
4	2.06005359217	5.60943220392	3.28730207402	4.65805034441	2.62485244811	2.3627970622	0.279158894567	1.02648660199	0.904198826278	-0.246430838747	0.00334282434422	0.272904811296	-0.277976693283	0.41910752756	-0.241081839373	0.778714168065	0.0879068842778	0.00921730018585	0.601933688265	0.0712578984785	0.683237675083	-20.7938269196	-4.55618543128	-46.7138577529
5	2.01075137068	-2.74778391864	2.03218445455	4.63352522331	-2.62892629305	2.32331161992	0.147380529012	0.29251842449	0.212044799796	-0.326810282544	-0.246350363106	-0.15460153098	-0.0928390391399	0.0702158243762	0.111100406194	0.455678479901	-0.00770419778974	-0.0116013451519	0.433509952826	0.0878251024841	0.348337861084	-19.8135306269	0.118620391948	-40.8297463134
6	6.96344310227	-3.20195236677	1.0332131516	7.90734955556	-2.40844904618	6.12979709485	-0.402220986209	-0.518200653533	0.967815239047	0.407144802632	0.206227568381	-0.407489380219	-0.774928978792	-0.252694277046	0.158058559409	0.425710543124	0.00922607209288	-0.0584074963095	0.427143019847	0.0524150966269	0.38666457274	-24.7449706943	6.90187851722	-38.2019703531
7	1.50887202853	0.0795390684106	-0.0240770228775	10.039949609	-5.45475796531	4.2660751402	-0.0884849722838	0.111134040662	0.156081211541	-0.581612842088	0.0470083707655	0.190785276108	0.0571417877402	-0.220814066779	0.122382930719	0.341131228956	-0.0264407457936	-0.0361265547097	0.363283282283	-0.0161043768686	0.255196976597	-16.6090316462	-6.84623067511	-18.8952761439
8	2.47773183826	-0.558726005535	0.116143188458	4.23430816761	0.206421397192	4.29190069608	-0.0308760720905	-0.125899894174	-0.109269371948	0.301379078828	0.00319388018196	-0.263948203015	0.111047377695	0.237053101671	0.0341880020508	0.304128321464	-0.0200567605335	-0.0332840397496	0.326047396503	0.0190307654903	0.268028580214	-8.57739633984	-21.1009911626	-3.06904908331
9	2.16784339754	1.41362806409	-0.211343215481	7.46359639562	-3.39147066851	4.28386070358	0.0672960675929	-0.0470552331525	0.626254130033	0.80321274996	-0.190314925697	0.026657896511	-1.05161603237	0.171694706127	0.135458774822	0.557585834124	-0.0930354423549	-0.0384011154642	0.387979935358	-0.023165609507	0.392888598399	-12.6939363043	5.7163740597	-11.9242809657
10	1.78408093101	1.70956325054	1.36038751075	9.10999661709	6.63345562168	5.50048447583	0.00654429202982	-0.106063991805	-0.179401442178	0.579760239723	0.202321664745	0.00844881047419	0.557349140972	0.0163797170529	-0.190006253974	0.349893629157	0.0113181641509	-0.0757456288429	0.305083622857	0.0578732254542	0.258771382855	-29.4780003757	-29.7446206766	19.2268112641
11	3.63195206964	-0.825607386953	2.91604076297	6.7976134039	1.08932533502	4.31360066059	-0.355098509931	-0.210925468948	0.555839811588	0.024980784314	0.179825614933	0.174142801089	-0.381866932046	0.0995652428948	0.184504361864	0.338647821276	-0.0261605594192	-0.0355155114123	0.227538525269	-0.00407765251946	0.315920828647	-22.8032323265	-4.41595918943	21.9001164315
12	4.5899906269	-1.17817253425	-1.86113849154	2.22024392829	1.07272251716	5.65090439286	0.118939810646	-0.0586264658876	0.536715070756	-0.233806013402	-0.0358360723074	0.139014662684	-0.897669975989	-0.31940458086	-0.103089670116	0.461933538477	0.0681023981608	-0.0901348583747	0.284178440755	-0.0259259952955	0.355744033811	-30.6370193784	-2.94116327024	16.8568203191
13	1.6721713839	0.0281894912379	-0.226890610148	1.88243933583	-0.386369179931	3.48060572708	0.0189858964115	0.031748975347	-0.0258616295624	-0.241495804862	-0.0769706992556	0.258483711475	-0.138340272962	-0.344072187518	0.0441881098375	0.320720740629	0.0320724774816	-0.107227748382	0.269968547897	0.00592922069086	0.313743990576	-38.3282592514	-13.2587167825	15.0804963901
14	1.12585473916	-0.486251769543	-0.838576134616	6.22462339714	3.79214875383	3.82424437117	-0.0237660920713	0.108264835948	-0.185158777136	-0.491522854658	0.0406898702584	0.0247316551536	-0.0250490909386	-0.186400944219	0.0121434854458	0.381063029355	-0.0291179989781	-0.0758213932068	0.286190962228	0.0328711018083	0.316860034563	-32.9245038977	-27.9403382859	7.71851491167
15	4.32396713887	0.66963854829	-0.857963767951	3.65892893302	-0.147861725936	5.75196039167	0.460597081333	0.776942219671	-0.690254218353	-0.112366121665	-0.355755662547	0.700494482294	0.108136260221	-0.748040505397	-0.129157252186	0.796281816257	0.112586499548	-0.0791404634587	0.760390134742	-0.136555850808	0.874490353812	-44.112719777	-33.1714699895	4.15879716134
16	0.484777731536	1.41476615034	1.82459656732	4.24098651802	5.01738725487	7.13302494641	-0.102707651915	-0.0374085663446	0.0481866831896	-0.137736048656	-0.261491844947	0.380211992825	0.0216234401869	-0.35706284787	0.368726721176	0.424004582517	-0.0815905931183	-0.103173587309	0.318564503147	0.0137752556487	0.411112350015	-39.369543584	-38.5983171771	7.4629469732
17	6.71128095606	-0.296893558233	-0.0217734377326	1.54085882131	0.000933868476668	4.14449820708	-0.0922373548738	0.226800464036	-1.13314303621	0.36019107315	0.105646078969	0.0974377953579	1.15529140046	0.55668706565	-0.0191278918872	0.648082124405	-0.00132100745004	-0.0933333666637	0.322706102493	-0.00812556824364	0.447520047139	-33.934901314	-47.4076007926	4.44950121262
18	2.5383382452	2.71268653298	1.08186612982	2.17158674096	1.77353940121	2.07152901186	-0.0461843255891	0.168954242745	-0.104003593123	-0.625752273403	0.0613898647542	0.422317684294	0.246031558146	0.019050703675	-0.0597191819852	0.413073932592	0.0345227577486	-0.0938748721851	0.326293455476	0.00985756100831	0.28104728088	-22.2746573039	-32.0932683353	21.5891280212
19	2.93594071387	0.599541359754	1.25394401709	4.9010982735	-0.0117545536465	3.95490533071	-0.0361977834556	-0.442300636973	0.158718748684	0.374293541516	0.070679065259	-0.257679779455	-0.155104515207	0.166721457078	-0.0324800908438	0.313340575491	0.0512569671109	-0.0070001711903	0.404756621679	-0.0560137729932	0.282533637866	-13.0639485251	-14.7054016068	38.5051537727
20	1.3700125908	0.853586472979	0.16748382819	3.88683779446	0.181188592651	1.78071366033	0.0611572058394	-0.12541350013	-0.145548548285	0.193416777977	0.111356074344	-0.0828656158391	0.261154199667	0.0595617895115	-0.160164314274	0.306150859823	0.078545238309	-0.0304193515621	0.374877486766	0.0137628978963	0.26223782413	-15.0220388151	-32.7452121481	31.797679553
21	3.28640299087	1.44818985501	0.868769273088	3.70995978371	1.4400352267	7.72968682772	0.20458895019	0.0650408377075	-0.993316551236	-0.863386892937	-0.109971046887	-0.331057478122	1.17373386053	1.02468154784	-0.0777746441408	0.859675077242	0.201315106415	-0.160198894885	0.652098232405	-0.0388159682007	0.604748457208	-11.6647529897	-48.4328601761	30.2608908749
22	4.08282310221	3.91261887657	0.249300981428	8.66275350804	0.446009637346	2.80089735124	0.0916750118611	0.185206737371	-0.847451606875	0.789217308807	0.266663550718	-0.62130733684	0.840779745092	0.011686558231	-0.356680457647	0.685957713775	0.125875407371	-0.0995290288665	0.420457445962	-0.0151105015067	0.439614643093	-19.4611921036	-50.4349159544	24.0464808044

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 18 through 58 )	A	A	18 - 58	1 - 41
2	2	chain 'A' and (resid 59 through 128 )	A	A	59 - 128	42 - 111
3	3	chain 'A' and (resid 129 through 223 )	A	A	129 - 223	112 - 206
4	4	chain 'A' and (resid 224 through 241 )	A	A	224 - 241	207 - 224
5	5	chain 'A' and (resid 242 through 269 )	A	A	242 - 269	225 - 252
6	6	chain 'A' and (resid 270 through 285 )	A	A	270 - 285	253 - 268
7	7	chain 'B' and (resid 18 through 59 )	B	D	18 - 59	1 - 42
8	8	chain 'B' and (resid 60 through 176 )	B	D	60 - 176	43 - 159
9	9	chain 'B' and (resid 177 through 284 )	B	D	177 - 284	160 - 267
10	10	chain 'C' and (resid 18 through 59 )	C	G	18 - 59	1 - 42
11	11	chain 'C' and (resid 60 through 76 )	C	G	60 - 76	43 - 59
12	12	chain 'C' and (resid 77 through 128 )	C	G	77 - 128	60 - 111
13	13	chain 'C' and (resid 129 through 178 )	C	G	129 - 178	112 - 161
14	14	chain 'C' and (resid 179 through 223 )	C	G	179 - 223	162 - 206
15	15	chain 'C' and (resid 224 through 241 )	C	G	224 - 241	207 - 224
16	16	chain 'C' and (resid 242 through 269 )	C	G	242 - 269	225 - 252
17	17	chain 'C' and (resid 270 through 287 )	C	G	270 - 287	253 - 270
18	18	chain 'D' and (resid 18 through 59 )	D	J	18 - 59	1 - 42
19	19	chain 'D' and (resid 60 through 138 )	D	J	60 - 138	43 - 121
20	20	chain 'D' and (resid 139 through 223 )	D	J	139 - 223	122 - 206
21	21	chain 'D' and (resid 224 through 241 )	D	J	224 - 241	207 - 224
22	22	chain 'D' and (resid 242 through 284 )	D	J	242 - 284	225 - 267

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