PDB-4om9: X-Ray Crystal Structure of the passenger domain of Plasmid encode...

ID or keywords:

Entry

Database: PDB / ID: 4om9

Title

X-Ray Crystal Structure of the passenger domain of Plasmid encoded toxin, an Autrotansporter Enterotoxin from enteroaggregative Escherichia coli (EAEC)

Components

Serine protease pet

Keywords

HYDROLASE / Beta-Helix / Peptidase / alpha-fodrin / EAEC / plasmid encoded toxin(PET)

Function / homology

Function and homology information

Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.3 Å

Authors

Meza-Aguilar, J.D. / Fromme, P. / Torres-Larios, A. / Mendoza-Hernandez, G. / Hernandez-Chinas, U. / Arreguin-Espinosa de Los Monteros, R.A. / Eslava-Campos, C.A. / Fromme, R.

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: X-ray crystal structure of the passenger domain of plasmid encoded toxin(Pet), an autotransporter enterotoxin from enteroaggregative Escherichia coli (EAEC).
Authors: Domingo Meza-Aguilar, J. / Fromme, P. / Torres-Larios, A. / Mendoza-Hernandez, G. / Hernandez-Chinas, U. / Arreguin-Espinosa de Los Monteros, R.A. / Eslava Campos, C.A. / Fromme, R.

History

Deposition	Jan 27, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 26, 2014	Group: Database references / Structure summary
Revision 1.2	Apr 2, 2014	Group: Database references
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4om9.cif.gz	377.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4om9.ent.gz	309.2 KB	Display	PDB format
PDBx/mmJSON format	4om9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4om9_validation.pdf.gz	431.5 KB	Display	wwPDB validaton report
Full document	4om9_full_validation.pdf.gz	463.3 KB	Display
Data in XML	4om9_validation.xml.gz	40 KB	Display
Data in CIF	4om9_validation.cif.gz	59.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/om/4om9 ftp://data.pdbj.org/pub/pdb/validation_reports/om/4om9	HTTPS FTP

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Related structure data

Related structure data	3szeS S: Starting model for refinement
Similar structure data	2o9j-d 6yso-1 5zmv-d 4uu0-d 2c88-d 2dqs-d 4j2t-d 3n5k-1 4ycn-d 3nal-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Serine protease pet

104 kDa, 1 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)	77.758, 95.926, 164.869
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Serine protease pet / Plasmid-encoded toxin pet Mass: 104055.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 042 / EAEC / Gene: EC042_pAA035, pet / Plasmid: pCEFN2 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 (pCEFN2) References: UniProt: O68900, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Serine protease pet / Plasmid-encoded toxin pet

Mass: 104055.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: 042 / EAEC / Gene: EC042_pAA035, pet / Plasmid: pCEFN2 / Production host:

Escherichia coli (E. coli) / Strain (production host): HB101 (pCEFN2)
References: UniProt: O68900, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.95 Å³/Da / Density % sol: 58.37 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 13 mg/ml protein in 50 mM Tris-HCL, 5 mM EDTA, pH 6.5 and 0.3 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2011
Radiation	Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9787 Å / Relative weight: 1
Reflection	Resolution: 2.3→41.46 Å / Num. all: 55562 / Num. obs: 55340 / % possible obs: 99.6 % / Redundancy: 25 % / B_iso Wilson estimate: 38 Å²

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: dev_1439)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Starting model: PDB ENTRY 3SZE

3sze

Resolution: 2.3→41.46 Å / SU ML: 0.29 / σ(F): 1.91 / Phase error: 27.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2628	2808	5.09 %
R_work	0.2203	-	-
obs	0.2224	55196	99.35 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→41.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7043	0	0	543	7586

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7146
X-RAY DIFFRACTION	f_angle_d	1.143	9657
X-RAY DIFFRACTION	f_dihedral_angle_d	16.041	2552
X-RAY DIFFRACTION	f_chiral_restr	0.046	1104
X-RAY DIFFRACTION	f_plane_restr	0.005	1267

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 (%)
2.3-2.3397	0.3422	148	0.2966	2600	X-RAY DIFFRACTION	100
2.3397-2.3822	0.3102	151	0.2754	2569	X-RAY DIFFRACTION	100
2.3822-2.428	0.3037	123	0.2604	2637	X-RAY DIFFRACTION	100
2.428-2.4776	0.2991	159	0.2492	2557	X-RAY DIFFRACTION	100
2.4776-2.5314	0.3288	137	0.247	2624	X-RAY DIFFRACTION	100
2.5314-2.5903	0.283	131	0.2395	2600	X-RAY DIFFRACTION	100
2.5903-2.6551	0.2951	146	0.2283	2592	X-RAY DIFFRACTION	100
2.6551-2.7269	0.298	132	0.2338	2618	X-RAY DIFFRACTION	100
2.7269-2.8071	0.302	154	0.2282	2598	X-RAY DIFFRACTION	100
2.8071-2.8977	0.2886	132	0.2229	2636	X-RAY DIFFRACTION	100
2.8977-3.0012	0.3107	144	0.2286	2613	X-RAY DIFFRACTION	100
3.0012-3.1213	0.2721	133	0.2237	2620	X-RAY DIFFRACTION	100
3.1213-3.2633	0.2472	142	0.2206	2607	X-RAY DIFFRACTION	100
3.2633-3.4353	0.2554	128	0.2035	2658	X-RAY DIFFRACTION	100
3.4353-3.6504	0.2282	155	0.2403	2578	X-RAY DIFFRACTION	99
3.6504-3.9321	0.3178	130	0.2831	2431	X-RAY DIFFRACTION	92
3.9321-4.3274	0.2457	144	0.2012	2625	X-RAY DIFFRACTION	98
4.3274-4.9527	0.1947	125	0.1616	2686	X-RAY DIFFRACTION	100
4.9527-6.2365	0.2356	147	0.1962	2698	X-RAY DIFFRACTION	100
6.2365-41.46	0.2373	147	0.2002	2841	X-RAY DIFFRACTION	100

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	0.8574	-0.925	-0.0115	1.0419	-0.1184	1.0611	-0.1428	-0.5365	0.0543	0.2192	0.193	-0.1143	0.2869	-0.2264	0.0004	0.3531	-0.0286	0.0021	0.5018	-0.025	0.3632	-26.8707	30.6624	-41.1825
2	2.0422	0.5057	-0.2666	0.5625	-0.2128	1.736	0.0735	0.3376	-0.022	0.0263	-0.0074	0.1089	-0.118	-0.1505	0.0001	0.3364	-0.0149	0.0231	0.4501	-0.0451	0.3692	-34.6612	27.1433	-61.8728
3	1.9781	0.2839	0.0321	0.1793	0.38	1.0208	0.0408	-0.4115	0.09	0.0892	-0.0595	0.0368	-0.0006	-0.3075	-0.0012	0.2757	-0.029	0.0148	0.4528	-0.0235	0.3335	-38.9959	30.1256	-47.9133
4	1.6594	-0.6239	0.6737	0.4436	0.881	1.7547	0.0996	0.764	-0.0742	-0.1248	-0.0828	0.029	0.1226	-0.0237	0.0528	0.3267	0.0382	0.0123	0.4636	-0.0444	0.2834	-15.7302	19.3243	-76.6067
5	1.1457	0.186	0.7752	0.5672	0.1809	0.6122	-0.0418	-0.0554	0.2949	0.0898	-0.0102	0.0393	-0.2322	-0.0863	0.0002	0.3064	0.0326	-0.0005	0.4284	-0.0071	0.2799	-2.863	26.9322	-62.6123
6	1.8943	-0.0723	0.4826	0.2658	-0.534	1.1096	0.0622	-0.1506	0.0711	0.1157	-0.0682	-0.1332	0.0426	0.1274	-0.0001	0.2931	0.0409	-0.0013	0.3393	-0.0481	0.3557	2.6575	26.6816	-51.1482
7	2.0978	-0.1915	-0.5982	0.0343	0.0947	0.2492	-0.7526	0.6458	-0.3963	-0.6378	0.4504	0.6558	-0.1283	0.3552	0.2013	0.3757	-0.032	-0.0138	0.495	-0.1438	0.9933	-22.8831	57.2962	-49.5012
8	0.4583	0.426	0.4234	0.753	0.6196	0.5322	-0.1056	-0.4257	0.5764	0.3395	0.1071	0.0699	-0.0533	0.0279	-0.0109	0.3511	0.0288	0.0477	0.5356	-0.1991	0.4926	-18.1115	43.708	-35.0565
9	1.873	-0.5138	1.8897	0.7296	-0.503	1.7068	0.0244	-0.1657	-0.0181	0.1452	-0.0331	-0.0368	0.0995	-0.0461	-0.0001	0.3808	0.0192	0.0031	0.4813	-0.0519	0.3521	7.1838	26.1275	-35.6488
10	0.3316	-0.292	-0.3184	0.2593	0.2966	0.3865	-0.5297	0.5267	0.4254	0.3641	-0.4474	0.3438	0.3867	-1.0521	-0.012	1.363	0.213	0.0428	1.0859	0.1176	0.7112	9.0517	1.8585	-25.3927
11	1.2492	-0.0901	-0.2461	0.6476	0.0325	0.3602	-0.033	-0.3464	-0.067	-0.0874	0.1701	0.0898	0.635	-0.3684	0.0722	0.7913	-0.0635	-0.2261	0.9335	0.1253	0.539	16.9138	18.1394	-17.8838
12	1.7775	-0.2925	0.0976	0.5348	-0.1972	0.0794	-0.0131	-1.0301	0.0687	0.6951	-0.198	-0.0914	0.6355	0.1344	0.0438	1.0534	0.0697	0.0046	1.0148	0.0514	0.2611	12.8982	17.5657	-10.6795
13	2.1952	-0.5167	0.772	0.2645	0.0134	0.5341	0.3776	0.2454	0.0605	-0.1385	0.479	0.3548	-0.1059	0.0481	0.2302	2.5468	-0.9479	0.4039	1.4465	0.0222	1.2059	18.6881	-0.6567	-16.2411
14	2.8541	0.5094	-0.9939	0.6855	-0.0566	0.5643	0.4927	-0.9303	-0.17	0.6204	-0.0569	-0.0647	0.3527	-0.3496	1.5333	1.1434	-0.1885	-0.357	1.3213	0.2058	0.6218	22.0759	16.0085	-4.3507
15	0.8201	1.3862	0.6636	2.6298	1.2055	0.5479	0.1576	-0.739	0.1199	0.5643	-0.5517	0.1647	0.0873	-0.3734	-0.2136	1.5438	-0.2217	-0.3128	1.5673	0.1364	0.6403	27.9221	13.5934	4.871
16	0.575	-0.0967	-0.4463	0.0511	-0.0301	0.6801	-0.1708	-0.0971	0.0351	-0.279	-0.1362	-0.1604	0.2384	0.1028	-0.6465	1.636	0.4414	-0.3224	1.3849	0.5966	0.8369	43.7325	3.2297	8.2311
17	9.9673	0.8096	-2.9379	2.2169	-0.456	0.8901	0.4038	0.3422	0.5338	-0.4533	1.1297	0.6144	0.3416	-0.4637	1.4891	1.2454	-0.1053	-0.4236	1.6309	0.2165	0.8356	24.2815	15.4122	12.2424
18	0.0338	0.0209	-0.0433	0.0169	-0.0047	0.0648	-0.1674	0.4677	-0.1362	0.3167	-0.0686	0.074	-0.8883	0.1686	0.0022	1.9536	-0.1715	-0.557	1.5478	0.4309	1.5225	29.6512	0.454	6.114
19	0.2123	-0.3031	-0.2702	1.4902	0.6843	0.411	0.1449	-0.4877	0.6393	0.4019	-0.3479	-1.4804	-0.9889	-0.7825	0.0094	2.1998	0.1445	-0.5983	2.0008	0.0229	1.155	31.0744	9.8479	12.5789
20	0.238	0.0373	-0.058	0.0845	0.0298	0.0506	0.5932	-0.0191	0.0743	1.1368	-0.047	0.8872	0.2943	0.0321	0.0024	1.6394	-0.1024	-0.2144	1.3445	0.1271	0.9255	21.5194	-1.7305	-4.4985

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 3:60)	A	3 - 60
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 61:134)	A	61 - 134
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 135:251)	A	135 - 251
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 252:408)	A	252 - 408
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 409:430)	A	409 - 430
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 431:528)	A	431 - 528
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 529:539)	A	529 - 539
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 540:576)	A	540 - 576
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 577:713)	A	577 - 713
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 714:724)	A	714 - 724
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 725:751)	A	725 - 751
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 752:770)	A	752 - 770
13	X-RAY DIFFRACTION	13	(CHAIN A AND RESID 771:786)	A	771 - 786
14	X-RAY DIFFRACTION	14	(CHAIN A AND RESID 787:853)	A	787 - 853
15	X-RAY DIFFRACTION	15	(CHAIN A AND RESID 854:880)	A	854 - 880
16	X-RAY DIFFRACTION	16	(CHAIN A AND RESID 881:888)	A	881 - 888
17	X-RAY DIFFRACTION	17	(CHAIN A AND RESID 890:906)	A	890 - 906
18	X-RAY DIFFRACTION	18	(CHAIN A AND RESID 907:922)	A	907 - 922
19	X-RAY DIFFRACTION	19	(CHAIN A AND RESID 923:941)	A	923 - 941
20	X-RAY DIFFRACTION	20	(CHAIN A AND RESID 943:964)	A	943 - 964

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