PDB-8cpk: Crystal structure of EtpA secretion domain from Enterotoxigenic E...

ID or keywords:

Entry

Database: PDB / ID: 8cpk

Title

Crystal structure of EtpA secretion domain from Enterotoxigenic Escherichia coli

Components

EtpA

Keywords

CELL ADHESION / Adhesin

Function / homology

Function and homology information

adhesion of symbiont to host cell surface via host membrane carbohydrate / extracellular region
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.76 Å

Authors

Ntui, C.M. / Schubert, W.D. / Fleckenstein, J.M.

Funding support

United States, 1items

Citation

Journal: Plos One / Year: 2023
Title: Structural and biophysical characterization of the secreted, beta-helical adhesin EtpA of Enterotoxigenic Escherichia coli.
Authors: Ntui, C.M. / Fleckenstein, J.M. / Schubert, W.D.

History

Deposition	Mar 2, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 10, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 24, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8cpk.cif.gz	1013.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8cpk_validation.pdf.gz	450.1 KB	Display	wwPDB validaton report
Full document	8cpk_full_validation.pdf.gz	468.7 KB	Display
Data in XML	8cpk_validation.xml.gz	72.5 KB	Display
Data in CIF	8cpk_validation.cif.gz	95.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cp/8cpk ftp://data.pdbj.org/pub/pdb/validation_reports/cp/8cpk	HTTPS FTP

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Related structure data

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

Deposited unit

A: EtpA

B: EtpA

C: EtpA

D: EtpA

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

1

A: EtpA

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

2

B: EtpA

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

3

C: EtpA

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

4

D: EtpA

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

Unit cell

Length a, b, c (Å)	37.711, 64.188, 123.957
Angle α, β, γ (deg.)	91.610, 90.890, 90.020
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	EtpA Mass: 38847.605 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: etpA / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q29XT7
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.93 Å³/Da / Density % sol: 36.27 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, hanging drop Details: 0.1 M Na2 citrate pH 5.5, 20% (w/v) PEG 4000, 20% (v/v) isopropanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2020
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.76→64.1625 Å / Num. obs: 112100 / % possible obs: 96.99909 % / Redundancy: 3.4 % / B_iso Wilson estimate: 23.58 Å² / CC_1/2: 0.999 / Net I/σ(I): 8.3
Reflection shell	Resolution: 1.76→1.79 Å / Num. unique obs: 5450 / CC_1/2: 0.297

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
PHENIX	1.20.1_4487	refinement
xia2		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.76→61.95 Å / SU ML: 0.2697 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.5364
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2401	5491	4.92 %
R_work	0.2001	106100	-
obs	0.2021	111591	96.82 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.37 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→61.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10877	0	0	702	11579

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	11781
X-RAY DIFFRACTION	f_angle_d	0.7989	16064
X-RAY DIFFRACTION	f_chiral_restr	0.0621	1799
X-RAY DIFFRACTION	f_plane_restr	0.0066	2209
X-RAY DIFFRACTION	f_dihedral_angle_d	5.6065	1856

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 (%)
1.76-1.78	0.3951	209	0.3629	3332	X-RAY DIFFRACTION	90.17
1.78-1.8	0.3719	201	0.3511	3389	X-RAY DIFFRACTION	93.37
1.8-1.82	0.3571	216	0.3211	3393	X-RAY DIFFRACTION	95.55
1.82-1.85	0.3869	179	0.3112	3461	X-RAY DIFFRACTION	96.14
1.85-1.87	0.3331	151	0.292	3603	X-RAY DIFFRACTION	96.08
1.87-1.9	0.3202	147	0.2747	3570	X-RAY DIFFRACTION	96.12
1.9-1.92	0.304	176	0.2651	3451	X-RAY DIFFRACTION	96.31
1.92-1.95	0.3141	185	0.2444	3551	X-RAY DIFFRACTION	96.21
1.95-1.98	0.273	218	0.2358	3500	X-RAY DIFFRACTION	96.15
1.98-2.01	0.2692	160	0.2334	3522	X-RAY DIFFRACTION	96.46
2.01-2.05	0.2956	159	0.2286	3494	X-RAY DIFFRACTION	96.54
2.05-2.09	0.2824	168	0.2177	3621	X-RAY DIFFRACTION	96.88
2.09-2.13	0.2388	172	0.2087	3531	X-RAY DIFFRACTION	96.89
2.13-2.17	0.2373	187	0.1991	3500	X-RAY DIFFRACTION	96.52
2.17-2.22	0.2749	183	0.1965	3601	X-RAY DIFFRACTION	96.9
2.22-2.27	0.2286	148	0.1927	3479	X-RAY DIFFRACTION	96.75
2.27-2.33	0.2523	147	0.1977	3636	X-RAY DIFFRACTION	97.15
2.33-2.39	0.2597	177	0.2003	3562	X-RAY DIFFRACTION	97.4
2.39-2.46	0.2698	195	0.2117	3490	X-RAY DIFFRACTION	97.1
2.46-2.54	0.2848	160	0.2167	3629	X-RAY DIFFRACTION	97.88
2.54-2.63	0.265	172	0.2005	3543	X-RAY DIFFRACTION	97.69
2.63-2.73	0.2594	198	0.2045	3600	X-RAY DIFFRACTION	98.01
2.73-2.86	0.2634	214	0.2017	3576	X-RAY DIFFRACTION	98.24
2.86-3.01	0.2122	211	0.192	3525	X-RAY DIFFRACTION	98.26
3.01-3.2	0.2213	230	0.1805	3574	X-RAY DIFFRACTION	98.02
3.2-3.44	0.2225	215	0.1734	3578	X-RAY DIFFRACTION	98.65
3.44-3.79	0.1869	154	0.1558	3644	X-RAY DIFFRACTION	98.67
3.79-4.34	0.1954	216	0.1569	3556	X-RAY DIFFRACTION	98.74
4.34-5.47	0.1876	171	0.1664	3601	X-RAY DIFFRACTION	98.05
5.47-61.95	0.2174	172	0.2247	3588	X-RAY DIFFRACTION	98.1

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	2.74776414471	0.00595331042171	0.335192989333	1.80305582914	-0.218228696216	2.02360586645	0.0110991062309	0.346320633875	-0.0621014263022	-0.112573133551	-0.0591413747331	-0.100557549448	-0.0557684914839	0.226145927815	0.0499206299521	0.204210362257	-0.0163184361572	0.00262198947727	0.269649375095	-0.0194371402847	0.173321331858	2.89473565602	2.00631633376	-17.1356184799
2	2.10707608806	-0.498440012227	-0.00237766240332	2.67639032739	-0.181402601117	1.95476178929	0.00902474351007	0.106386700346	-0.0915266734208	0.124315179797	-0.0108174965903	0.132515868478	0.0851468533316	0.000487480221495	1.47561174301E-5	0.121882147571	0.0051610736171	-0.0132696441889	0.146360684748	-0.010885951304	0.118701198649	-1.38781470382	-1.21953476883	-5.14285664015
3	3.57461264758	0.402077187988	0.390549417765	5.67117923044	-0.176715876593	2.57565349416	-0.0863901987652	0.145357617857	0.00856852654456	0.116931855902	-0.00651831488863	0.659849627863	0.111226362576	-0.347749114916	0.0784794990496	0.161292738891	-0.0359651204065	0.0246551747628	0.265732079399	-0.0379100847405	0.249656739543	-10.4278810353	-4.43779949968	0.777417371207
4	2.98264298322	0.136739690604	0.100711434617	3.17347463704	0.510062698469	2.59332911716	-0.0644048211493	0.0382015503606	-0.279636814313	-0.030737900271	-0.0088807599835	-0.0527120285348	0.416094037161	-0.0553945250876	0.0650913838019	0.209207617229	0.006025915283	0.000637740975728	0.154721807405	-0.00965428333518	0.12269691247	-1.30077333823	-5.12045252249	10.6136347955
5	3.03974449086	-0.314643679783	0.169864574978	5.97654863006	-0.0220223362345	3.407448536	-0.0249325225428	-0.0542715289823	0.0947529604822	0.170467458052	-0.0218313525869	0.488562462425	0.0538024795571	-0.4829027829	0.0637674384788	0.152016693775	-0.0229845580055	0.0169161509444	0.234004680939	-0.0159272040437	0.139208509173	-7.15057062918	1.49680978559	14.6710212865
6	1.71481331845	-0.338841234664	-0.0238338718959	4.22020078258	-0.0580476928861	2.79246541918	0.0270125711074	0.00635064059603	0.0169404127629	-0.0378901612868	-0.080994594087	0.22375020442	0.217941739261	-0.356163119852	0.0376167128465	0.165041999998	-0.01664334028	0.0143456951597	0.238289863812	-0.0179538283671	0.143782340731	-9.1616604744	1.16768546803	21.4801567117
7	2.74819040694	-0.240613629474	-0.113897785517	3.91525874392	-0.44523984274	2.65547959407	-0.0593837258091	-0.181631673122	0.093938680264	0.331549306205	0.0150550618695	-0.0422106789262	-0.0509991730794	-0.100855960398	0.0539230500231	0.223519742544	-0.00457668822169	-0.0101521438083	0.247107558769	-0.01428868563	0.128869508874	-6.52866688277	3.08764893268	29.4253964541
8	2.59802590244	1.25646087581	0.193849690006	9.6592324822	1.02348182812	2.61236524062	0.100108436828	0.0110184325803	-0.000918331296779	0.476464273124	-0.351248386743	0.23743978311	0.310546954433	-0.554637806218	0.192120080789	0.315780400894	-0.0129025017977	0.0608557388853	0.334618861115	-0.00483165965453	0.156173302676	-9.50445059465	-2.29145947056	34.2185731062
9	3.07571021801	0.352679704499	0.660376341272	3.71744702946	0.334566711897	3.64846427242	0.0664371575349	-0.641533394871	-0.128745793502	0.3662372821	-0.00309803445512	-0.058224241718	0.0243024252305	0.177533702886	-0.0418737169921	0.217644476514	-0.00880460180016	0.0260578187226	0.339996220759	-0.0255110122212	0.231220242358	-29.724755692	-6.56185631947	95.0335805479
10	1.87882395288	0.304983300922	-0.0539443363177	2.47168009127	0.364479523134	2.70860323121	0.106809227433	-0.173338584238	0.0837001558024	0.120161117313	-0.083685029032	0.0648233825596	0.0207692269991	0.105773059421	-0.017049704757	0.128326123329	-1.2849966767E-5	0.00180717798658	0.20016908845	0.00247449080387	0.13651052635	-27.1874159983	-4.02896857628	87.9304990062
11	2.53244053764	0.5980652045	-0.443274550484	3.2858011926	-0.672706149742	2.53259304571	-0.068541793397	-0.155799714457	-0.20098352975	0.0214201308941	0.03743664683	-0.226247322268	0.13889445756	0.151175616035	0.0281914417012	0.15821804509	-0.0136946618527	0.0277322267394	0.201267053426	-0.0260772414681	0.216563001388	-22.6167970174	-5.18908883696	82.6474971143
12	3.78855070979	-0.486660698196	-0.646403168347	2.58430371869	0.0265653556721	2.38183364437	-0.0325823976374	0.0865508460832	-0.01775519887	-0.0864188606189	0.0874150948155	0.250976287218	0.0178858421638	-0.247536041117	-0.0444967317888	0.145260877995	-0.0325210602323	0.00593955341548	0.174901707355	-0.00335658372601	0.156445885698	-25.9352776531	-0.921524159658	75.9961523362
13	3.27663493365	-0.212011996181	-0.957814298068	3.66050869548	0.386922270254	2.49309588323	-0.0446949338938	0.233189427867	0.0614879950555	-0.12531479272	0.0430114491624	0.0892590285144	-0.143486377246	-0.310099317497	-0.0124175021155	0.186966353623	-0.014687363541	-0.0108676388014	0.195726417693	-0.0283745470639	0.125569435954	-21.9378546021	0.818076677364	66.2821435124
14	3.54368851527	1.19760989083	-0.470551830683	5.54924561349	0.094030261715	3.60705198159	-0.0915515036438	0.30952197203	-0.154427486187	-0.0203725407521	0.109326216608	0.441750096946	0.123273068983	-0.466398724425	-0.00435079565425	0.181033152152	-0.0171902453436	0.00872769629818	0.233104062914	-0.0255739598268	0.140297599558	-18.3226277774	-4.78536998773	56.6272949092
15	1.96919524659	-0.908547234786	-0.428738660065	3.78558650581	-0.069924176628	3.2032804341	-0.0912844372739	0.455707366064	-0.0499316229159	-0.218566523204	0.00221429254895	0.295074730611	0.0610752542942	-0.556935010895	0.0598291786991	0.210897132005	-0.0528483270743	-0.0035831923827	0.378201213959	-0.0282787051936	0.190762907333	-18.3873206383	-4.67398069806	49.728696794
16	3.0545713985	0.356405344109	-0.0600209202344	4.37138338173	0.797585051464	3.23845486342	0.0231458846803	0.419930484225	-0.161704165122	-0.0924045562065	-0.0115020478672	-0.0653608463798	0.0949763127407	-0.329133155352	-0.0494917362226	0.181877433265	-0.00600909109724	0.00632343634311	0.229891083079	-0.00782886241965	0.136880425431	-11.6568069968	-7.93224944336	45.9264014019
17	4.00517784283	0.202064832057	0.409750525599	7.54093534095	-0.0766214316905	3.2007967804	-0.0526628113231	0.26631624834	0.0237881266722	-0.467887687422	0.13355116487	0.129852598675	-0.067762373602	-0.58001553565	-0.0743665759577	0.393158627367	-0.0114078893048	0.0183795608361	0.312871202281	0.0230161988091	0.130607555112	-11.0772359276	-2.13535028575	40.2888494367
18	2.83660955605	-0.479479317285	-1.63423327413	1.89312226505	0.42795576189	2.67207802213	0.034180619953	0.0334249380873	-0.00180161149161	0.00147321367355	0.0429661373317	-0.0219397084759	-0.00245322545001	0.0727253009814	-0.0611197338626	0.134167826421	-0.0101357815515	-0.0185901410817	0.138431500966	-0.00516899495564	0.20338938695	-17.0906839353	29.6472238203	-3.324697994
19	1.81694824329	0.766063271107	-1.43412434268	1.01902172662	-0.308476392412	3.81357659022	0.0659054804687	-0.319666607085	-0.00720450166712	0.170915935402	-0.117056249143	-0.142569150281	-0.0920133873633	0.558619322732	0.0319208922666	0.181337023024	0.00246114966173	-0.0317737313232	0.247823743701	0.00992864293896	0.2256810834	-28.6990080509	28.0275524133	24.9300183449
20	3.52762865077	0.47041217167	0.501941171698	2.1902702718	-0.110504784783	2.26583092741	0.16915793656	-0.519141572497	0.0351751798005	0.270308318768	-0.16703327045	0.254000506743	-0.0375494147541	-0.233690310398	-0.00665855290169	0.20757614864	-0.0380489126213	0.0438491639057	0.291177989917	-0.0108328292563	0.230136321017	-9.08285764191	33.8217716735	94.9601384306
21	0.924081369951	0.35104775876	0.668972469805	1.70541344391	-0.35821543317	1.93094347848	0.030706800711	-0.0297604647491	-0.110779517691	-0.116143019839	0.00513570052584	0.0119227493386	0.138026044074	0.0545040310847	-0.0326971995025	0.150555079887	-0.0136753936531	0.0174312220863	0.178022847285	-0.0148833536053	0.206101559075	-3.12220510437	29.1860093423	77.7135767895
22	1.55955601846	0.416763979972	-0.272485598591	3.32493411992	0.115573114274	4.111551341	-0.0232577743937	0.0644854995857	-0.038454346537	-0.14581020426	0.0121980380493	-0.0935288652439	0.155953116318	0.362613260073	-0.00580952619432	0.132098973719	0.0182607807815	-0.0155637980063	0.192238538173	-0.0326269434175	0.164263501223	1.59462907107	33.2438930828	53.0404164937

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 -3 through 70 )	A	A	-3 - 70	1 - 74
2	2	chain 'A' and (resid 71 through 160 )	A	A	71 - 160	75 - 164
3	3	chain 'A' and (resid 161 through 191 )	A	A	161 - 191	165 - 195
4	4	chain 'A' and (resid 192 through 228 )	A	A	192 - 228	196 - 232
5	5	chain 'A' and (resid 229 through 256 )	A	A	229 - 256	233 - 260
6	6	chain 'A' and (resid 257 through 310 )	A	A	257 - 310	261 - 314
7	7	chain 'A' and (resid 311 through 359 )	A	A	311 - 359	315 - 363
8	8	chain 'A' and (resid 360 through 380 )	A	A	360 - 380	364 - 384
9	9	chain 'B' and (resid -2 through 25 )	B	B	-2 - 25	1 - 28
10	10	chain 'B' and (resid 26 through 70 )	B	B	26 - 70	29 - 73
11	11	chain 'B' and (resid 71 through 97 )	B	B	71 - 97	74 - 100
12	12	chain 'B' and (resid 98 through 160 )	B	B	98 - 160	101 - 163
13	13	chain 'B' and (resid 161 through 228 )	B	B	161 - 228	164 - 231
14	14	chain 'B' and (resid 229 through 276 )	B	B	229 - 276	232 - 279
15	15	chain 'B' and (resid 277 through 310 )	B	B	277 - 310	280 - 313
16	16	chain 'B' and (resid 311 through 359 )	B	B	311 - 359	314 - 362
17	17	chain 'B' and (resid 360 through 380 )	B	B	360 - 380	363 - 383
18	18	chain 'C' and (resid -2 through 191 )	C	C	-2 - 191	1 - 194
19	19	chain 'C' and (resid 192 through 380 )	C	C	192 - 380	195 - 383
20	20	chain 'D' and (resid -2 through 70 )	D	D	-2 - 70	1 - 73
21	21	chain 'D' and (resid 71 through 228 )	D	D	71 - 228	74 - 231
22	22	chain 'D' and (resid 229 through 380 )	D	D	229 - 380	232 - 383

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