PDB-6ox6: Crystal structure of the complex between the Type VI effector Tas...

ID or keywords:

Entry

Database: PDB / ID: 6ox6

Title

Crystal structure of the complex between the Type VI effector Tas1 and its immunity protein

Components

PA14_01140
Tas1

Keywords

TRANSFERASE /

type VI secretion / bacterial warfare / (p)ppApp /

alarmone /

Pseudomonas aeruginosa /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

protein secretion by the type VI secretion system /

: /

NAD+ glycohydrolase / toxin sequestering activity / NADP+ nucleosidase activity / membrane => GO:0016020 /

membrane
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.17 Å

Authors

Ahmad, S. / Stogios, P.J. / Skarina, T. / Whitney, J. / Savchenko, A. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201200026C	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201700060C	United States

Citation

Journal: Nature / Year: 2019
Title: An interbacterial toxin inhibits target cell growth by synthesizing (p)ppApp.
Authors: Ahmad, S. / Wang, B. / Walker, M.D. / Tran, H.R. / Stogios, P.J. / Savchenko, A. / Grant, R.A. / McArthur, A.G. / Laub, M.T. / Whitney, J.C.

History

Deposition	May 13, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 18, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 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.title / _citation.year
Revision 1.2	Nov 20, 2019	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	Dec 11, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ox6.cif.gz	149.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6ox6.ent.gz	108.8 KB	Display	PDB format
PDBx/mmJSON format	6ox6.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/ox/6ox6 ftp://data.pdbj.org/pub/pdb/validation_reports/ox/6ox6	HTTPS FTP

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Related structure data

Related structure data	6ottC C: citing same article (ref.)
Similar structure data	5ojr-4 3hp7-d 3jxz-d 5ojr-3 4jh4-d 6y0e-d 4jh1-d 5ojp-2 4v16-d 4g3n-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP96613 TargetTrack: IDP96614

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tas1

B: PA14_01140

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	66.631, 66.631, 148.307
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2
Space group name Hall	P4nw2abw

#1: Protein	Tas1 Mass: 45821.449 Da / Num. of mol.: 1 / Fragment: UNP residues 22-460 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: CGU42_21755, IPC3_19385 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus / References: UniProt: A0A232D9K2, UniProt: Q9I739*PLUS
#2: Protein	PA14_01140 Mass: 9274.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: CGU42_21760, EGJ96_33750, EQH76_16385, IPC3_19390, PA34_000540 Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus / References: UniProt: A0A090A233
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 1.48 Å³/Da / Density % sol: 16.79 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M sodium acetate, pH 4.5, 0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic, cryoprotectant: 20% v/v ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2017
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection	Resolution: 2.17→50 Å / Num. obs: 18200 / % possible obs: 98 % / Redundancy: 9.2 % / R_merge(I) obs: 0.083 / R_pim(I) all: 0.025 / Net I/σ(I): 33.39
Reflection shell	Resolution: 2.17→2.21 Å / R_merge(I) obs: 0.322 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 856 / CC_1/2: 0.974 / R_pim(I) all: 0.125 / % possible all: 96.4

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Processing

Software

Name	Version	Classification
PHENIX	1.15_3448	refinement
PHENIX	1.15_3448	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.17→49.56 Å / SU ML: 0.2074 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.0806

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2307	1593	4.97 %	RANDOM
R_work	0.185	-	-	-
obs	0.1872	17817	94.98 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 42.9 Å²

Refinement step

Cycle: LAST / Resolution: 2.17→49.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2105	0	28	304	2437

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0091	2221
X-RAY DIFFRACTION	f_angle_d	1.0044	2998
X-RAY DIFFRACTION	f_chiral_restr	0.0682	307
X-RAY DIFFRACTION	f_plane_restr	0.0074	410
X-RAY DIFFRACTION	f_dihedral_angle_d	20.3947	850

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	% reflection R_free (%)	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.17-2.24	0.2849	129		0.2285	2339	80.36
2.24-2.32	0.2379	128		0.2228	2536	87.17
2.32-2.41	0.2093	143	0.2841		2756	94.15
2.41-2.52	0.2478	140		0.2179	2660	91.26
2.52-2.66	0.2861	148		0.2155	2917	99.22
2.66-2.82	0.2593	152		0.2163	2869	99.38
2.82-3.04	0.3299	153		0.2114	2929	99.55
3.04-3.35	0.2323	152		0.1842	2826	97.54
3.35-3.83	0.2012	152		0.1526	2899	99.74
3.83-4.82	0.1798	152		0.1424	2846	98.01
4.82-49.56	0.1997	144		0.1871	2892	98.51

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	1.80219603627	0.760407397859	-0.334424357236	1.4427903202	-1.03326591994	0.830761118533	-0.229132649846	-0.0432474097089	-0.0255382539763	0.318880316947	0.190174705056	0.121905617386	0.234364540689	-0.0507811778997	-0.23465182188	1.16094226628	0.136147882054	0.0799372120435	0.291792843886	0.0966930754288	0.290908912207	36.1339202117	49.8215530836	89.1238896309
2	3.39944002241	0.33021811905	0.685689493044	1.97510085986	-0.24956418371	1.69691921205	-0.165394830138	-0.244283649426	0.137831022389	1.13260466926	0.0202689593883	0.176950603118	0.0743761021471	-0.143441338671	0.1127859647	0.945580605167	0.0497296944816	0.177405478123	0.22482379486	0.0185547582028	0.375498480964	35.4589456747	57.7170256369	86.8671866751
3	1.92130905798	-0.525341989146	0.52817610125	0.564691076206	0.455594278918	0.998982793722	-0.420734422912	-0.111797755934	0.0410885857795	0.575569497505	0.155178700415	0.256247867188	0.409141807568	-0.0115915321949	0.215717725868	0.697059973342	0.0621370096889	0.129285290234	0.184837047243	0.028973351946	0.267602867772	38.1988406394	55.1775936349	82.374778244
4	1.86922500191	-0.561854308214	0.694596692295	5.49819661725	-1.62036322277	1.31620648237	-0.122933142097	-0.190839005347	0.119394981412	0.315030045422	0.0266564026814	-0.57857702484	-0.0445236203595	0.118994442426	0.0938731105682	0.438898840322	0.29514470883	-0.0607816884751	0.355726475174	-0.0164749845722	0.412004494002	53.45327341	55.697571627	79.2837212916
5	2.86199351371	-1.17756248335	1.59938164073	6.34847367796	-2.25224237891	1.32756931935	-0.148884895674	0.109596033312	-0.121053931552	-0.275186931958	0.135805754075	-0.640337447844	0.865077776005	0.258646664723	0.0940244543933	0.4035048546	0.124557933039	0.0903810018326	0.25138335892	0.0202515643245	0.222638883864	45.9427698348	61.8963469613	74.4074458052
6	5.34049564084	4.91703398728	-0.755144804619	9.18067336519	-2.3748070103	0.712622634961	0.0773550675467	-0.20206847874	-0.320201810441	0.134109440017	-0.102790823609	0.101427496062	0.578075944005	0.0810628909548	0.0170356027937	0.849388742853	0.192454837044	0.0342552291157	0.280246796477	0.0286234333939	0.252068446236	43.2601409081	52.3784695576	84.4910695834
7	5.76891084369	-2.56622093028	-1.52129151846	7.28638121319	0.796228689962	6.10135428916	0.0925871474976	-0.348758652765	0.620763581109	0.626468483235	0.0318686651875	-0.152457825318	-0.262137830087	0.561803972166	-0.140461304016	0.343465968568	-0.060629896376	0.0264819376398	0.234411344256	0.00181320046121	0.285184736393	47.1626199318	74.0402368795	88.1458282251
8	5.6220087641	3.12066290458	5.81185555741	6.276991189	4.28146055939	7.07324337762	0.0979727629306	-0.213140270357	0.341947515784	0.438487854422	-0.0818657143908	0.229380731712	-0.298667883627	-0.367884061902	-0.0109448164669	0.254090310606	-0.00583900416125	0.123776279815	0.17193388451	0.0776132879554	0.308971654311	38.4182585281	75.3544839843	76.7291330214
9	5.07702779087	-0.812440502643	-1.05823192355	6.0438538147	-4.2552772122	3.67063922666	0.263458654753	0.248188138059	0.583933248361	0.112526460431	-0.167236932579	0.807959539252	-0.465814818926	-0.714239385709	-0.066192075511	0.18050238652	0.0105585758537	0.0922689409582	0.312959283365	0.101077955284	0.32270134307	28.7320237022	72.3273767399	63.9143484154
10	5.09115706592	1.24831143452	1.84969536816	4.8815824677	0.616555196903	7.02132244548	-0.285679148236	0.865072285977	0.525202548134	-0.303731878042	0.180062924491	-0.39446389519	-0.635578102489	0.627856455468	0.0857696124279	0.20092151747	-0.0576070817783	0.0619048588016	0.215555906194	0.0986899286001	0.340921666126	44.8834318597	76.7322318458	69.8187848089
11	3.2668512561	1.18373745544	1.54535724908	9.84041330916	-2.16015756666	1.77471415473	0.280100624424	1.09532341377	0.664955672815	-0.77580872502	-0.38026470525	-1.06666358038	0.132093037717	1.05695378453	0.137857741651	0.219449050832	0.0301806063848	0.046829935434	0.489789854275	0.0348276067726	0.255997701636	36.9355965138	66.8703299267	61.9378656158
12	6.33747341138	2.95497414951	-5.45173336841	4.41549470896	-4.10304542302	5.49210356178	0.30314410143	0.247799557276	0.23534901102	-0.250602663811	0.0776261454579	-0.205353520778	-0.409286760033	0.0730711492848	-0.347686156335	0.246067451439	-0.0200376510459	0.0299113502158	0.627824420388	0.121107655815	0.330402105583	32.0225150044	65.8449088622	54.1802965705
13	5.70536436866	-1.2678178879	5.30529144068	3.85064956244	-2.14342136867	6.91910415575	-0.0164010306242	0.644651819044	-0.250469886947	0.169195294487	-0.23038996011	-0.0787397877462	0.554737619276	0.366713202598	0.217485714512	0.263463020703	0.0348697974825	0.114229243693	0.291461920358	0.00568945328693	0.225126248564	37.7336423721	54.921016915	65.6337818272
14	2.57510161535	-0.389951498635	-0.886300311789	5.3113502075	-0.474063252388	2.89696801039	-0.130973628918	0.598302828091	-0.0680558845955	-0.131622378346	-0.00983405681646	0.765056968072	0.33256580108	-0.62596778138	0.120128447661	0.14396876734	-0.0841569446541	0.0342534234684	0.336759285374	-0.0594068025712	0.388068346798	27.526660063	56.6164622833	61.6349949922
15	1.91789933224	1.08247752991	0.0777897915287	0.611154904792	0.0520614448768	0.16435080974	-0.204158643379	0.139317575284	-0.0455985617427	0.258007511468	-0.167070336443	0.773352547823	0.376428083547	-0.271343862804	0.301740208306	0.315670667819	-0.11164826754	0.179336063763	0.334351157625	-0.0496711316555	0.500433311466	26.1768234688	55.2352137208	67.855237511
16	7.81399365334	3.14638791427	0.282368133583	6.02248459428	2.0849130064	0.906129982798	-0.0295957249168	-0.384893926184	-0.174870000171	0.676823581167	-0.0287822751329	0.137816536372	0.221299100114	0.0532382252733	0.0584823834624	0.164831386951	0.0104539232739	0.0581800234359	0.17137389109	0.0607816478207	0.172701841506	35.8573715649	61.9360384918	70.289048974
17	0.60973643967	1.41347404856	0.643274352709	7.07193286805	5.97665425494	5.97908541658	-0.142519712733	0.434867382623	0.109458316708	-0.0248713348001	0.217604166956	-0.248457929956	0.249127664624	0.549712212234	-0.0361896600529	0.15567226281	-0.0265198612741	0.0630941930223	0.447036279239	-0.0515820162735	0.333427778017	39.9714745583	56.0629246555	59.2875703928
18	7.20998759186	-2.22375994649	0.924612262177	3.47034460717	-5.26627629859	9.03464913139	0.049547466665	0.573859042024	-0.495308758111	-0.446736466847	-0.213857871303	-0.0235573660599	0.542143271642	0.145674858034	0.153643194826	0.32718106794	-0.0732916370144	0.0276886410665	0.426417057893	-0.203293352483	0.42984237833	34.7828397052	47.0479299801	59.2864407754

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 243 through 272 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 273 through 296 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 297 through 315 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 316 through 336 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 337 through 353 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 354 through 365 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 366 through 394 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 395 through 410 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 411 through 418 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 419 through 436 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 2 through 6 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 7 through 13 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 14 through 21 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 22 through 38 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 39 through 52 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 53 through 61 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 62 through 66 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 67 through 77 )

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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About Yorodumi

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

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Mar 5, 2020. Novel coronavirus structure data

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Jul 12, 2017. Major update of PDB

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Yorodumi