PDB-8vl8: Salmonella enterica Typhimurium taxis to serine and repellents (T...

ID or keywords:

Entry

Database: PDB / ID: 8vl8

Title

Salmonella enterica Typhimurium taxis to serine and repellents (Tsr) ligand-binding domain with L-Ser, pH 7

Components

Methyl-accepting chemotaxis protein

Methyl-accepting chemotaxis proteins

Keywords

SIGNALING PROTEIN /

chemoreceptor /

chemotaxis / MCP / Tsr

Function / homology

Function and homology information

chemotaxis / transmembrane signaling receptor activity /

signal transduction /

plasma membrane
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Glenn, S. / Baylink, A.

Funding support

United States, 1items

Citation

Journal: eLife / Year: 2024
Title: Human Serum is a Potent Chemoattractant for Enterobacteriaceae Species Associated with Gastrointestinal Bleeding
Authors: Glenn, S. / Gentry-Lear, Z. / Shavlik, M. / Harms, M.J. / Asaki, T.J. / Baylink, A.

History

Deposition	Jan 11, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 3, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vl8.cif.gz	355.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8vl8.ent.gz	242.3 KB	Display	PDB format
PDBx/mmJSON format	8vl8.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/vl/8vl8 ftp://data.pdbj.org/pub/pdb/validation_reports/vl/8vl8	HTTPS FTP

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Related structure data

Related structure data	3atp 8fyv
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 (8) #190 - Oct 2015 Two-component Systems similarity (4)

Deposited unit

A: Methyl-accepting chemotaxis protein

B: Methyl-accepting chemotaxis protein

C: Methyl-accepting chemotaxis protein

D: Methyl-accepting chemotaxis protein

E: Methyl-accepting chemotaxis protein

hetero molecules

95.7 kDa, 5 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&software
38.4 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&software
38.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Methyl-accepting chemotaxis protein

hetero molecules

E: Methyl-accepting chemotaxis protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	126.022, 74.771, 128.931
Angle α, β, γ (deg.)	90.000, 116.140, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

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Protein , 1 types, 5 molecules ABCDE

#1: Protein	Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins Mass: 18932.043 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: 14028 / Gene: G0L35_02695 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A707MW50

#1: Protein

Methyl-accepting chemotaxis protein /

Methyl-accepting chemotaxis proteins

Mass: 18932.043 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: 14028 / Gene: G0L35_02695 / Production host:

Escherichia coli K-12 (bacteria) / References: UniProt: A0A707MW50

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Non-polymers , 5 types, 243 molecules

#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-SER / SERINE / Serine Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C₃H₇NO₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.88 Å³/Da / Density % sol: 57.3 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1.5 ul protein at 7 mg per ml in 50 mM Tris pH 7.5, 1 mM EDTA, 150 mM NaCl, 0.5 ul of 6 mM L-serine, and 1.5 ul 1.62 M potassium phosphate pH 7 PH range: 7-7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 23, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9774 Å / Relative weight: 1
Reflection	Resolution: 2.12→62.38 Å / Num. obs: 72723 / % possible obs: 98.3 % / Redundancy: 6.1 % / B_iso Wilson estimate: 21.26 Å² / CC_1/2: 0.977 / Net I/σ(I): 5.4
Reflection shell	Resolution: 2.12→2.18 Å / Redundancy: 4.7 % / Num. unique obs: 4009 / CC_1/2: 0.568 / % possible all: 88.5

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
DIALS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→61.5 Å / SU ML: 0.347 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.5126
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2734	2641	3.63 %
R_work	0.2257	70082	-
obs	0.2275	72723	99.44 %

Solvent computation

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

Displacement parameters

B_iso mean: 35.97 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→61.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5524	0	53	220	5797

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0126	5700
X-RAY DIFFRACTION	f_angle_d	1.2141	7726
X-RAY DIFFRACTION	f_chiral_restr	0.0515	842
X-RAY DIFFRACTION	f_plane_restr	0.0107	1021
X-RAY DIFFRACTION	f_dihedral_angle_d	19.6751	2078

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 (%)
2.5-2.55	0.3456	133	0.2947	3686	X-RAY DIFFRACTION	99.82
2.55-2.59	0.3581	147	0.2789	3705	X-RAY DIFFRACTION	99.84
2.59-2.65	0.3731	140	0.2829	3744	X-RAY DIFFRACTION	99.85
2.65-2.7	0.3591	151	0.2891	3699	X-RAY DIFFRACTION	99.74
2.71-2.77	0.3744	125	0.272	3666	X-RAY DIFFRACTION	99.32
2.77-2.84	0.3548	149	0.2672	3688	X-RAY DIFFRACTION	99.92
2.84-2.91	0.2866	123	0.2596	3754	X-RAY DIFFRACTION	99.9
2.91-3	0.3022	156	0.2524	3671	X-RAY DIFFRACTION	99.74
3-3.1	0.2973	118	0.2405	3711	X-RAY DIFFRACTION	99.66
3.1-3.21	0.3203	162	0.2506	3700	X-RAY DIFFRACTION	99.79
3.21-3.34	0.3131	117	0.244	3687	X-RAY DIFFRACTION	99.56
3.34-3.49	0.2324	148	0.2261	3687	X-RAY DIFFRACTION	99.28
3.49-3.67	0.309	139	0.219	3682	X-RAY DIFFRACTION	99.04
3.67-3.9	0.2464	134	0.2052	3572	X-RAY DIFFRACTION	97.45
3.9-4.2	0.211	145	0.1802	3637	X-RAY DIFFRACTION	97.83
4.2-4.62	0.2175	145	0.1724	3692	X-RAY DIFFRACTION	99.66
4.63-5.29	0.1797	131	0.1782	3716	X-RAY DIFFRACTION	99.74
5.29-6.67	0.238	135	0.2117	3705	X-RAY DIFFRACTION	99.87
6.67-61.5	0.2146	143	0.1894	3680	X-RAY DIFFRACTION	99.53

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	2.99016769845	0.363574774388	0.369775734581	4.61121039123	-0.471509942181	2.92103353575	-0.258729033066	0.518889869264	0.622443578632	-0.348397776819	0.1296128431	0.110022030277	-0.162395135967	0.313742503894	0.104893234994	0.104499030539	0.00741074127134	-0.0514363893053	0.205544633618	0.0525241163673	0.187913938369	22.9323979656	13.8084659014	45.7169530141
2	2.36617741735	5.19805048333	-3.24156662254	5.64473281818	-2.65907378885	5.26423650436	-0.14197501729	0.947658564485	0.239181341226	-0.196083009513	0.113334071494	-0.0379798613052	-0.0471159274797	0.0568874044444	0.112398857998	0.179650995696	0.125076326614	-0.0478354532741	0.296787022624	-0.00858557737061	0.219072705675	21.4406012851	9.50445750794	39.7678978284
3	4.48649505847	1.84513405873	0.171405527433	1.95992169659	0.743361057774	2.65311100436	-0.428913052253	0.568137843759	0.012943988767	-0.696690874244	0.202128835441	-0.0477193736353	-0.0133250348647	0.449348273999	0.10925999442	0.101234777198	0.0526355642806	-0.016974720919	0.348532191435	0.0452580786479	0.13388059641	33.5775973058	9.32632397977	45.7745569669
4	7.70900271592	5.70389967857	-2.72138060417	6.98643304131	-4.44944106982	6.71520386003	0.403260734966	-0.291748488415	1.08446820392	0.66227749859	-0.229828784755	0.390282487018	-1.49081853788	0.530453237244	-0.0966584520224	0.384744570935	-0.105285199609	-0.0385782977535	0.388250250626	-0.0225914697929	0.31176092745	36.843487309	22.8997210477	50.4937908587
5	2.06034458483	-0.183456383997	-0.053779886721	4.84523371267	-2.22580696832	2.32037430056	-0.167493191223	0.186660582047	0.155101736802	0.240063210308	0.113469412907	-0.517869230406	-0.260580313673	-0.199974758843	-0.00020987120183	0.100064058742	-0.0184419659015	-0.0378158116346	0.178197607527	-0.0129864913687	0.167774479664	20.0492633868	15.5880450715	54.9897920998
6	0.960937853967	0.453927328197	0.0377121670064	8.61723082376	-6.55130756566	5.97562609803	-0.0950734808263	-0.204101987147	0.343294782808	0.743097386675	-0.384765005051	-0.479693660398	-0.945006810916	0.24447761265	0.424951235761	0.247396705208	-0.0333202226227	-0.0954460529522	0.268206003651	-0.0892956603766	0.333364379295	19.8446521219	23.3637394886	60.6429335358
7	2.07678215587	-0.970462863008	0.0496658230471	1.24526976201	1.19530695618	1.8490344683	0.56137216286	0.0365668212835	0.474028741114	0.348791671814	0.306831282191	-0.400058027089	-0.695360310541	0.0369549098281	-0.514342765262	1.35635511274	-0.327215137437	-0.245958892675	0.0369218043321	0.0979380387071	0.945118369827	21.4065762469	43.4671576121	46.6474209251
8	1.30956579145	-0.00816705509172	0.350404291107	7.15151559155	-4.0854360236	3.94217861064	0.0425692172964	-0.363116870963	0.182974763622	0.206124512801	0.00515349972939	0.687920530362	-0.261365825546	-0.201396324524	-0.129660464754	0.10703740129	0.0749535697343	-0.0103941464319	0.260964763624	-0.0600593357968	0.198746295812	9.26045751146	21.6536310844	53.9492812647
9	4.17644217309	0.485347053832	-0.589934936001	7.07372914279	-1.5023453095	4.77484296375	-0.0974026750295	-0.0990576378196	0.291690602215	-0.134980488739	-0.556584724628	-1.17513950339	-1.11945061081	0.879889908618	0.654693707762	0.443947509395	-0.0825257203265	-0.104698076441	0.366570903927	0.105012689641	0.312101173759	19.5685825833	29.9813064052	41.5373887037
10	2.10893262554	0.545319525299	-0.837969836984	1.64867717616	-0.396111201822	3.37474273756	0.133693411544	0.420871474985	-0.0537558466127	-0.267040429548	-0.157607039303	-0.0429363396676	0.436888336306	0.212584695838	0.0190679090303	0.307789729293	0.0749254699721	-0.0938918685965	0.467795624672	0.0400997361415	0.0203511588929	1.08966648006	25.7891799237	27.228399008
11	6.25852616431	-4.37828303971	0.225018138667	5.55679591302	0.785128224573	2.69639477399	0.665866168688	0.880085877045	-0.673469455557	-0.635908053099	-0.565807701806	0.50530332688	0.255724206007	0.178539719013	-0.118672079873	0.360698689177	-0.0337249782186	-0.0755498366416	0.455031577941	0.0219572013411	0.123848218344	-3.82852414516	22.5653108093	23.3237547925
12	5.38256068902	2.22526962909	3.8753395884	8.06369925165	-1.4844937768	4.12334871285	-0.121915730603	2.32315601035	-1.79407154299	-1.0389063647	-0.434761781611	-0.71076035031	1.07383151403	2.09263485579	0.535195383884	0.59009519963	0.180243862707	0.109278112854	0.76749721211	-0.0506796966829	0.597530103461	21.4711840666	8.79773884907	22.4308658443
13	8.65399136398	-3.84210860446	-0.413873682261	2.22841651461	-0.329968415667	0.730138954014	0.0579984104403	0.436288381227	-0.601313569263	-0.0575041228969	-0.078449264186	0.316030198635	0.231939388883	-0.0946506884226	0.00345359063264	0.268711868242	-0.023942151897	-0.102683931137	0.204587693835	-0.0335159371824	0.172792410053	-0.182791452919	16.8472874926	34.2767874417
14	7.49938239468	-1.88849411689	-4.33155655299	5.19849452269	1.60609961499	5.66780131093	0.315304367844	1.08928800202	0.233439303326	-0.413705285169	-0.0885988678512	-0.986399952704	0.249556028777	0.367311129913	-0.154679175207	0.243491330217	0.140699633838	0.0129734156194	0.602666603749	-0.0290441237565	0.295631895763	17.0123129028	19.821375443	30.9470833679
15	3.33625615976	-0.589508283473	-0.524025375949	1.94473030339	-0.496086986933	3.07776305445	0.0729543018	0.0650112938862	0.130010252003	-0.256582378431	-0.0720831149323	-0.13910255246	0.00177033149816	0.480167621586	-0.00813138418682	0.184407500988	0.0381693537246	-0.0236935909166	0.258267582094	-0.00585124555518	0.0959609583233	4.5775151352	32.8173438594	32.8606007487
16	9.15586536717	1.09072915305	-6.97649453632	2.8452206108	-1.05749406663	2.10567704087	0.0614687665615	-0.174291914642	0.341587059602	-0.13713761156	0.05179609917	-0.426194004448	-0.00171427303662	0.859499645628	0.0108136856546	0.257495681484	-0.0961276638297	-0.0627573793551	0.467785942368	-0.0147213764879	0.242301340474	12.1079424337	38.6233909317	34.0749945445
17	3.88420116805	0.259194858494	2.29683639364	3.40779784352	-1.63149422722	2.29478444707	-0.0784048572479	1.12994930081	-0.66367278793	-0.98225683371	0.207201598535	-1.07186094707	-0.217324652872	1.34846835087	-0.0671197941093	0.581959505122	-0.238658245701	0.209212702209	1.00115039507	-0.0690475597876	0.487656336561	25.4857519275	37.3421440225	14.1200640685
18	4.56753954284	1.15269367488	-2.35627176146	0.934963233609	-0.220596661709	4.88429361288	-0.156607332149	0.61610310086	-0.0385412428517	-0.0655099110083	0.0872165143097	-0.119355657339	0.0981790884351	0.48018552409	0.0435332424369	0.291721122293	0.0249144462916	-0.0528294337042	0.381371892765	0.0267196556216	0.135358008037	6.29792298172	38.746924639	21.8434388841
19	1.54229244808	-0.250069037666	-0.45083236444	4.21088590972	-2.17372957612	3.67313086749	0.0353763023123	0.0489126236666	-0.0721475202086	-0.857059650276	-0.181712647638	0.0527629199405	0.146249675351	-0.138360739879	0.144454437228	0.409219698239	0.0121219137526	-0.0459953378963	0.378298263127	-0.0583175779633	0.128680257029	-4.89570408273	37.4920550686	-0.545226561253
20	2.59283977697	5.23225662146	1.65447813086	2.00122864342	3.42581955225	1.09932998575	-0.365721072206	-0.183253531464	0.978465856818	-0.296734665716	0.188529138091	0.842645092025	-2.28814863392	-0.52705959645	0.224969602744	0.950996988095	0.0850375779762	-0.0115404676569	0.452813809412	0.0398145187948	0.47447460482	-2.24589262259	58.5623978503	-9.2276536025
21	2.65123752637	0.488910420681	-0.420523221482	7.03226129363	-7.894661568	8.79500358779	-0.121856809197	-0.21162861285	-0.0877271360593	-0.609772256804	0.48605385823	0.278458948803	0.537432555649	-1.44631763528	-0.440496853905	0.501424137142	0.0142895333352	-0.0687211775044	0.587066401823	-0.00644606360993	0.167580960253	-12.9482887353	36.1743023176	-2.38948451221
22	1.79396739169	-0.71217627496	0.446417952667	1.71129347023	-2.46971475305	3.94090272235	0.135449826639	-0.0543321895626	0.0416953736474	-0.157334706734	-0.0336265396803	0.611789513006	-0.135207160805	-0.547363804461	-0.0972773373193	0.40535540709	0.0666607148482	-0.032323212054	0.553632281113	-0.0342777704011	0.0996679233014	-10.4549968613	36.8533028811	9.01023209904
23	1.5803966761	-0.726893845905	0.599834625063	8.39921922764	-3.09391334326	3.25380812581	0.373813014888	-0.0236720260974	-0.464029862669	-1.65017107712	-0.283870106047	-0.0359819012661	0.627418272784	0.0287655419577	-0.111871395475	0.583860977798	0.0283467225236	-0.112594609241	0.453528274216	0.00122175767222	0.245410393474	-1.33853334605	25.6328724915	10.3477233351

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 42 through 79 )	A	A	42 - 79	1 - 38
2	2	chain 'A' and (resid 80 through 109 )	A	A	80 - 109	39 - 68
3	3	chain 'A' and (resid 110 through 155 )	A	A	110 - 155	69 - 114
4	4	chain 'A' and (resid 156 through 201 )	A	A	156 - 181	115 - 140
5	5	chain 'B' and (resid 42 through 86 )	B	B	42 - 86	1 - 45
6	6	chain 'B' and (resid 87 through 110 )	B	B	87 - 110	46 - 69
7	7	chain 'B' and (resid 111 through 118 )	B	B	111 - 118	70 - 77
8	8	chain 'B' and (resid 119 through 155 )	B	B	119 - 155	78 - 114
9	9	chain 'B' and (resid 156 through 201 )	B	B	156 - 181	115 - 140
10	10	chain 'C' and (resid 43 through 79 )	C	C	43 - 79	1 - 37
11	11	chain 'C' and (resid 80 through 110 )	C	C	80 - 110	38 - 68
12	12	chain 'C' and (resid 111 through 118 )	C	C	111 - 118	69 - 76
13	13	chain 'C' and (resid 119 through 155 )	C	C	119 - 155	77 - 113
14	14	chain 'C' and (resid 156 through 201 )	C	C	156 - 181	114 - 139
15	15	chain 'D' and (resid 42 through 86 )	D	D	42 - 86	1 - 45
16	16	chain 'D' and (resid 87 through 110 )	D	D	87 - 110	46 - 69
17	17	chain 'D' and (resid 111 through 118 )	D	D	111 - 118	70 - 77
18	18	chain 'D' and (resid 119 through 201 )	D	D	119 - 181	78 - 140
19	19	chain 'E' and (resid 42 through 78 )	E	E	42 - 78	1 - 37
20	20	chain 'E' and (resid 79 through 86 )	E	E	79 - 86	38 - 45
21	21	chain 'E' and (resid 87 through 110 )	E	E	87 - 110	46 - 69
22	22	chain 'E' and (resid 111 through 155 )	E	E	111 - 155	70 - 114
23	23	chain 'E' and (resid 156 through 201 )	E	E	156 - 180	115 - 139

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