PDB-8ovt: Crystal structure of the ligand-free YeGT glycosyltransferase

ID or keywords:

Entry

Database: PDB / ID: 8ovt

Title

Crystal structure of the ligand-free YeGT glycosyltransferase

Components

YeGT glycosyltransferase

Keywords

TRANSFERASE / Glycosyltransferase / effector protein / nucleotide binding protein

Biological species

Yersinia enterocolitica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Wirth, C. / Hunte, C.

Funding support

Germany, 2items

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: Tyrosine-modifying glycosylation by Yersinia effectors.
Authors: Schneider, S. / Wirth, C. / Jank, T. / Hunte, C. / Aktories, K.

History

Deposition	Apr 26, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 15, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jun 5, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ovt.cif.gz	569 KB	Display	PDBx/mmCIF format
PDB format	pdb8ovt.ent.gz	394.4 KB	Display	PDB format
PDBx/mmJSON format	8ovt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ovt_validation.pdf.gz	457.5 KB	Display	wwPDB validaton report
Full document	8ovt_full_validation.pdf.gz	461.3 KB	Display
Data in XML	8ovt_validation.xml.gz	41 KB	Display
Data in CIF	8ovt_validation.cif.gz	56.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ov/8ovt ftp://data.pdbj.org/pub/pdb/validation_reports/ov/8ovt	HTTPS FTP

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Related structure data

Related structure data	8ovsC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: YeGT glycosyltransferase

B: YeGT glycosyltransferase

C: YeGT glycosyltransferase

D: YeGT glycosyltransferase

hetero molecules

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

1

A: YeGT glycosyltransferase

hetero molecules

defined by author
Evidence: gel filtration, indicate that YeGT is monomeric in solution
34.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: YeGT glycosyltransferase

hetero molecules

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

3

C: YeGT glycosyltransferase

hetero molecules

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

4

D: YeGT glycosyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	156.854, 156.854, 154.964
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
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+3/4 #3: y+1/2,-x+1/2,z+1/4 #4: x+1/2,-y+1/2,-z+1/4 #5: -x+1/2,y+1/2,-z+3/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

#1: Protein	YeGT glycosyltransferase Mass: 33958.883 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: Y2wildboar1B / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.58 Å³/Da / Density % sol: 65.64 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10 mM Tri-sodium citrate, 16% PEG 6000.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→49.1 Å / Num. obs: 57009 / % possible obs: 96.4 % / Redundancy: 38.6 % / CC_1/2: 1 / R_merge(I) obs: 0.188 / R_pim(I) all: 0.045 / Net I/σ(I): 17.1
Reflection shell	Resolution: 2.3→2.52 Å / R_merge(I) obs: 2.598 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2860 / CC_1/2: 0.85 / R_pim(I) all: 0.58

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
autoPROC		data processing
STARANISO		data scaling
PHASER		phasing
MxCuBE		data collection
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→49.06 Å / SU ML: 0.3004 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.8514
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.245	2998	5.26 %
R_work	0.2042	53976	-
obs	0.2063	56974	66.25 %

Solvent computation

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

Displacement parameters

B_iso mean: 61.97 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→49.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9177	0	32	220	9429

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0017	9412
X-RAY DIFFRACTION	f_angle_d	0.4191	12680
X-RAY DIFFRACTION	f_chiral_restr	0.0397	1352
X-RAY DIFFRACTION	f_plane_restr	0.0035	1638
X-RAY DIFFRACTION	f_dihedral_angle_d	18.2583	3607

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 (%)
2.3-2.34	0.2659	15	0.2812	360	X-RAY DIFFRACTION	9.26
2.34-2.38	0.2996	27	0.2949	430	X-RAY DIFFRACTION	11.42
2.38-2.42	0.3063	29	0.3098	508	X-RAY DIFFRACTION	13.32
2.42-2.47	0.3958	25	0.2852	593	X-RAY DIFFRACTION	15.31
2.47-2.52	0.2443	45	0.2982	790	X-RAY DIFFRACTION	20.75
2.52-2.57	0.3234	75	0.3123	1134	X-RAY DIFFRACTION	29.82
2.57-2.63	0.2737	64	0.2913	1366	X-RAY DIFFRACTION	35.52
2.63-2.7	0.3332	75	0.3033	1582	X-RAY DIFFRACTION	40.82
2.7-2.77	0.3438	118	0.2984	1953	X-RAY DIFFRACTION	51.11
2.77-2.85	0.35	161	0.3092	2552	X-RAY DIFFRACTION	66.64
2.85-2.95	0.3284	207	0.3054	3460	X-RAY DIFFRACTION	90.45
2.95-3.05	0.3363	244	0.2921	3794	X-RAY DIFFRACTION	99.04
3.05-3.17	0.3115	176	0.2753	3882	X-RAY DIFFRACTION	99.98
3.17-3.32	0.3185	194	0.2474	3884	X-RAY DIFFRACTION	100
3.32-3.49	0.274	221	0.2272	3894	X-RAY DIFFRACTION	100
3.49-3.71	0.242	229	0.2079	3867	X-RAY DIFFRACTION	99.98
3.71-4	0.2292	255	0.1785	3873	X-RAY DIFFRACTION	99.98
4-4.4	0.1997	216	0.1499	3911	X-RAY DIFFRACTION	100
4.4-5.03	0.1977	211	0.1462	3958	X-RAY DIFFRACTION	100
5.03-6.34	0.2342	195	0.1874	4011	X-RAY DIFFRACTION	99.98
6.34-49.06	0.1839	216	0.1702	4174	X-RAY DIFFRACTION	99.43

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	8.87742893924	-5.57260754243	5.39469106684	7.55188558834	-0.442718429293	5.59573951095	0.397781287139	-0.108642717813	1.49515102906	0.00659668461269	0.185531823737	-0.513181585055	-0.999837717165	-0.113506069273	-0.530938552203	0.824568854798	-0.158799402417	0.379111502005	0.643911286627	0.0431593547885	0.758870153289	-34.2910598551	-9.10033747285	-23.7343409889
2	1.8663774718	-0.394462425938	0.506984638279	0.577546092398	-0.463477910718	1.38901476988	0.384230132861	-0.723681987849	0.209521699582	0.735333701713	-0.154788843841	-0.327205075701	-0.0273179667685	0.0676392984896	0.347388372443	0.73620873051	-0.585069750061	-0.292523119806	1.05222755994	0.192054276671	0.299643996421	-5.21173680322	-36.1172593683	-5.72303373877
3	3.15104253629	-0.318184869829	1.29601691804	4.06435473478	1.02708533184	2.59786907692	0.254055394013	-0.00261131901491	0.149716896383	0.212543918176	-0.353812378229	0.217479296196	-0.198928916109	0.439926623838	0.0335031725283	0.467304868379	-0.331185950957	0.0125937311544	0.797471629681	0.0439095409522	0.247695967113	-18.9330560389	-32.5514093347	-15.8021519519
4	2.1816431724	-2.41191480916	-0.050964480317	2.89086966682	-0.424763871067	1.03967565324	0.459687307086	-0.395796100247	-0.541292604928	0.578779175353	-0.120536556821	0.907490688771	0.257549310222	-0.869328150437	0.55587258929	0.977075449789	-0.698571833686	0.0444927287821	1.17621249781	0.0565912864104	0.446769444357	-24.0922539184	-41.930411697	-4.62306474691
5	5.36646317459	-2.94983982107	2.56908333105	2.32477382366	-1.67974039537	2.28775869395	0.572813383928	-0.0536645343186	0.266413945174	0.176024253362	-0.353847257321	0.30380060092	-0.205030481132	0.377879844808	-0.232590446599	0.424904116151	-0.168630778355	0.198372100681	0.428656143183	-0.0282801476934	0.500342165556	-34.0538015428	-23.2788455185	-26.6956338203
6	4.00328913111	-1.33691941538	-1.21177772464	1.87709537473	2.40782153477	3.16669423828	0.308227106592	0.37403935521	-0.151371076808	0.741005969407	-0.474913349469	-0.192945071368	0.24574066886	0.679540277443	0.0868636752434	0.555327454609	-0.321948845358	-0.00703679906879	0.917354083658	0.0816295772678	0.237769230678	-14.3455931203	-31.2376314979	-20.7225417278
7	1.72026025157	-1.32107111584	-1.17029178247	3.15203084165	1.49321672721	2.98310966166	0.0201934901403	0.0188899086722	-0.336201277636	-0.107911772128	0.0405817302763	0.0790834460449	0.255437155691	-0.0681901521297	-0.0680822265249	0.280293193689	-0.0357753730645	0.00416285680195	0.195078398935	0.0417818989873	0.214283190257	-46.7155138827	-69.6757978517	8.66950959712
8	1.11332693576	-0.858652989178	-0.815882838356	1.28122994051	1.68326775571	3.17478688396	0.414431131043	-0.0299433780045	0.423662467301	-0.606134484761	0.211723022975	-0.450064069346	-0.586716084478	0.134220653789	-0.533584978021	0.52485117748	-0.0370146600084	0.196089477314	0.278322753077	0.0437848476722	0.33031495848	-47.3512784446	-50.91944446	13.6590616507
9	1.53954307559	-2.75509301822	-1.46480965802	6.77592486262	2.77899640075	3.47660740782	-0.144272858531	-0.112775625081	-0.0681734494987	0.414548307765	0.204988096384	0.119505862343	0.0998426921951	-0.166044967457	-0.0313334028981	0.303512710112	-0.043431666915	0.104012854738	0.312371478494	0.107034549104	0.263244856925	-58.2156124323	-52.8109870739	27.6463657844
10	2.12734372102	1.44004966348	-0.817092507204	0.951444041145	-0.753166807961	1.66414851887	0.209296941623	-0.0575939030939	-0.406845135683	-0.142111290035	-0.455996393727	-0.630681698619	0.0649410403756	0.732676729562	0.182340060075	0.279039665193	0.130629742283	0.0185669745164	0.9135918919	0.0102425407948	0.498923678817	-7.8020210766	-43.3771761001	-38.0788896808
11	2.93969854843	1.45398140063	-1.35199292998	4.36036671192	-1.62590858955	2.63155571905	0.205008874632	0.460629623454	0.252991718652	-0.484349064565	0.00749956787008	-0.261559140798	-0.129361994388	0.122059737963	-0.200295257077	0.441514155191	0.0237021510089	0.143647478768	0.890562836243	0.0677216455776	0.321361402371	-8.66094886511	-29.1944323756	-52.3755104497
12	3.88102956921	-0.973504267291	-0.57005767858	3.4516416976	1.24471636448	5.26732213336	0.258601266298	-0.0654749583737	-0.428739421531	0.0349485580931	-0.253497910138	-0.35828972685	-0.433389176597	0.901486584444	-0.0394091611215	0.305794914818	0.0453099581917	0.020353338618	1.00421494827	0.148391406837	0.482099371934	-4.75297003925	-38.2594809348	-36.5247570422
13	3.06220372586	0.678814992247	-2.29738242543	6.08601332525	0.624284759422	3.49294798181	0.277489975313	0.000117387878501	0.0353993047187	-0.207372019097	-0.0378771657964	-0.48011708994	-0.0476893464165	0.0938508631998	-0.196446753484	0.207369102605	0.0354877384455	0.00270969130462	0.800734944994	0.00819543550122	0.242217640971	-17.5235421518	-40.7673581039	-35.9909372504
14	1.33784127317	0.631155073175	-0.0643396638616	7.45109765397	-4.09584989251	3.86445383085	0.206334313876	0.691733263153	0.218037157907	-0.288677486839	0.252186147067	0.756278425696	-0.172886920731	-0.537337910852	-0.450427796495	0.244648320183	0.0829637959571	-0.00365603720606	0.751286707657	0.0173897716495	0.328922069448	-25.4041486478	-37.6254541431	-43.8526304983
15	3.38646040947	2.64718210056	0.346785651493	4.54332638223	-1.01834977279	1.20391044134	0.883029803763	-0.616794913732	-0.041393783038	1.00607635488	-0.736493212802	-0.0605620258547	-0.0300371087334	0.559993263927	-0.135118870489	0.353662125317	-0.0478948838086	-0.0753487131322	0.543274314924	-0.0532987885158	0.279100605626	-31.495162555	-59.0383296272	-19.743014176
16	4.94566141199	3.98335568091	-3.06745233083	6.23309258694	-2.27110639495	1.91648558304	0.703147029641	0.126523057289	-0.88704846898	0.340483045413	-1.25201152129	-0.561606128557	-0.088841553305	1.00677494256	0.496853783127	0.254087705023	0.0605608110994	-0.0913105935158	0.785071449179	0.0245644203952	0.545804079906	-18.5834555448	-55.8034494106	-26.1885438813
17	2.50374944138	1.0729831664	-0.489211143255	6.92188421229	5.28583326531	4.83838049975	0.550012858959	-0.528285229835	0.36252199595	-0.481838424302	-0.535085735231	-0.412868101574	-0.632599016682	1.13278917523	-0.145371698154	0.458435833415	-0.101442778876	0.0936209916964	1.05974454863	0.126435346023	0.444591790547	-10.5790529311	-34.3784161096	-31.396791924
18	3.77355590713	2.96133702922	1.14780883961	3.86536896764	2.43075929436	2.53171591556	0.19780079687	0.039241570632	0.801086886119	-0.373456945564	-0.236163316004	0.541945621669	-0.398813089419	-0.108396138791	0.0379031429494	0.364027760509	0.0745616552002	0.0306401018495	0.437342455857	0.183105345039	0.540780829205	-66.462232388	-32.6216828115	-37.986260321
19	4.08178386688	-0.769230040859	-0.722944696185	2.06344767711	1.52170685186	3.96781474277	0.22965084944	0.417805147757	-0.271043878185	-0.104023638208	-0.424162464332	0.688331041804	0.83113036452	-1.19276146358	0.141150130273	0.458339365866	-0.157005496048	-0.222755015679	0.733721176107	0.0657410589713	0.491099797986	-80.5885917539	-54.6529730347	-43.0516784471
20	2.88544688569	1.66272521938	2.05488574099	3.50560847931	0.249735617705	3.45127878028	0.0991657341087	0.879563454616	0.0321017741743	-0.674196335165	0.243708982655	0.157549653102	0.149767953909	-0.00870509868805	-0.218852716047	0.432680679671	0.05229603867	-0.147275935842	0.709862046247	-0.0390939683397	0.274233171571	-69.1288011922	-51.9547254384	-52.1562869672
21	3.54748662006	1.33698332447	0.2227797347	3.58930724646	0.57271373383	4.22540393455	0.243319455584	-0.0218068073903	0.457299925349	-0.109205025811	0.0167425291149	0.0981344251461	0.0489584497425	-0.172503938695	-0.197656626537	0.189863384388	0.0593935174825	-0.0404419496788	0.313230072636	0.0313501278344	0.273793320951	-66.9545547148	-42.2604156273	-36.2909442872
22	6.56224174208	-2.00406371529	1.84993745274	7.79938974269	0.606661743379	4.46466818278	0.191147249591	0.781977516923	-0.52320574864	0.0933164843531	0.114195342874	-1.17941958814	0.473090340871	1.10267938502	-0.245485500058	0.332030578863	0.111753647985	-0.0496183793489	0.635165309539	0.0146750433912	0.418301150446	-54.1165692204	-48.7571712569	-47.1236231372
23	2.94767856728	2.64284947891	0.891955647713	4.88116429305	1.91384160893	2.70871976181	0.563695734248	-0.147312303242	0.490642947297	0.0563779185457	-0.034766506242	-0.0850761877819	-0.363355387271	0.227316933487	-0.432836623424	0.282759916385	-0.0886941935409	0.211802298075	0.462918119914	0.0240533913411	0.534080477847	-50.6574209997	-27.4131913409	-26.5963225531
24	3.21753694077	2.39563138679	2.99150141722	6.16958929953	6.84382262862	8.89543037498	0.711713752337	-0.613532574967	0.904600636062	-0.00754831715768	-0.841762222037	0.876602800377	-0.369596737341	-0.860065731477	0.160439454896	0.364209253926	-0.013607709655	0.15282540583	0.377235502827	0.0474404484357	0.817683155004	-61.3582387968	-25.7249250817	-27.577159763
25	2.40901436695	0.935160949463	-0.754214097332	7.38769783662	-7.09752530672	8.85310562099	0.483239058377	-0.601916522248	-0.376288947867	-0.410641925077	0.307292871231	-0.219884582005	0.555647975591	-0.626433950361	-0.587049022711	0.336710355425	-0.074364187832	-0.232426074984	0.525201696126	0.0754373262137	0.443289396121	-69.0395942985	-47.3728116628	-31.0240162995

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 15 through 28 )	A	A	15 - 28	1 - 14
2	2	chain 'A' and (resid 29 through 162 )	A	A	29 - 162	15 - 148
3	3	chain 'A' and (resid 163 through 195 )	A	A	163 - 195	149 - 181
4	4	chain 'A' and (resid 196 through 221 )	A	A	196 - 221	182 - 207
5	5	chain 'A' and (resid 222 through 279 )	A	A	222 - 279	208 - 265
6	6	chain 'A' and (resid 280 through 301 )	A	A	280 - 301	266 - 287
7	7	chain 'B' and (resid 16 through 195 )	B	B	16 - 195	1 - 181
8	8	chain 'B' and (resid 196 through 255 )	B	B	196 - 255	182 - 241
9	9	chain 'B' and (resid 256 through 299 )	B	B	256 - 299	242 - 285
10	10	chain 'C' and (resid 16 through 74 )	C	C	16 - 74	1 - 59
11	11	chain 'C' and (resid 75 through 144 )	C	C	75 - 144	60 - 129
12	12	chain 'C' and (resid 145 through 162 )	C	C	145 - 162	130 - 147
13	13	chain 'C' and (resid 163 through 195 )	C	C	163 - 195	148 - 180
14	14	chain 'C' and (resid 196 through 237 )	C	C	196 - 237	181 - 222
15	15	chain 'C' and (resid 238 through 272 )	C	C	238 - 272	223 - 257
16	16	chain 'C' and (resid 273 through 286 )	C	C	273 - 286	258 - 271
17	17	chain 'C' and (resid 287 through 301 )	C	C	287 - 301	272 - 286
18	18	chain 'D' and (resid 16 through 51 )	D	D	16 - 51	1 - 36
19	19	chain 'D' and (resid 52 through 91 )	D	D	52 - 91	37 - 76
20	20	chain 'D' and (resid 92 through 144 )	D	D	92 - 144	77 - 129
21	21	chain 'D' and (resid 145 through 195 )	D	D	145 - 195	130 - 180
22	22	chain 'D' and (resid 196 through 221 )	D	D	196 - 221	181 - 206
23	23	chain 'D' and (resid 222 through 272 )	D	D	222 - 272	207 - 257
24	24	chain 'D' and (resid 273 through 286 )	D	D	273 - 286	258 - 271
25	25	chain 'D' and (resid 287 through 301 )	D	D	287 - 301	272 - 286

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