PDB-4edi: Disulfide bonded EutL from Clostridium perfringens

ID or keywords:

Entry

Database: PDB / ID: 4edi

Title

Disulfide bonded EutL from Clostridium perfringens

Components

Ethanolamine utilization protein

Keywords

TRANSPORT PROTEIN /

bacterial microcompartment / Eut / BMC shell protein

Function / homology

Function and homology information

bacterial microcompartment /

cobalamin binding / structural molecule activity /

metal ion binding
Similarity search - Function

Biological species

Clostridium perfringens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.998 Å

Authors

Thompson, M.C. / Cascio, D. / Crowley, C.S. / Kopstein, J.S. / Yeates, T.O.

Citation

Journal: Protein Sci. / Year: 2015
Title: An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein.
Authors: Thompson, M.C. / Cascio, D. / Leibly, D.J. / Yeates, T.O.

History

Deposition	Mar 27, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 10, 2016	Group: Database references
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4edi.cif.gz	361.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4edi.ent.gz	303.8 KB	Display	PDB format
PDBx/mmJSON format	4edi.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/ed/4edi ftp://data.pdbj.org/pub/pdb/validation_reports/ed/4edi	HTTPS FTP

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Related structure data

Related structure data	4fdzC 4tm6C 4tmeC 3i82S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4u6i-d 4tlh-d 6arc-d 6ard-d 4fdz-d 4tme-d 6p4m-d 6p4r-d 6tyn-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
Related items in Molecule of the Month	#114 - Jun 2009 Vaults similarity (4) #165 - Sep 2013 Designed Protein Cages similarity (4)

Deposited unit

A: Ethanolamine utilization protein

B: Ethanolamine utilization protein

C: Ethanolamine utilization protein

hetero molecules

71.2 kDa, 3 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)	86.747, 86.747, 251.681
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Ethanolamine utilization protein / EutL Mass: 23716.703 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CPE0900, eutL / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: Q8XLZ0
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 245 / 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: 3.33 Å³/Da / Density % sol: 63.03 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 5% PEG8000, 8% ethylene glycol, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.97949 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2010

Radiation

Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 1.998→100 Å / Num. obs: 65257 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / B_iso Wilson estimate: 25.677 Å² / R_merge(I) obs: 0.053 / Χ²: 1.006 / Net I/σ(I): 18.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.998-2.07	4	0.218	6436	1.051	1	99.4
2.07-2.15	4	0.167	6506	1.067	1	99.9
2.15-2.25	4	0.13	6476	1.033	1	99.6
2.25-2.37	4	0.106	6489	1.071	1	99.3
2.37-2.52	4	0.087	6500	1.019	1	99.5
2.52-2.71	4	0.066	6554	0.974	1	99.5
2.71-2.99	4	0.054	6573	0.921	1	99.6
2.99-3.42	4	0.047	6584	0.984	1	99.2
3.42-4.31	3.9	0.044	6523	0.984	1	97
4.31-100	3.7	0.034	6616	0.955	1	93

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 53.19 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	61.34 Å
Translation	2.5 Å	61.34 Å

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHASER	2.1.4	phasing
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.1	data extraction
ADSC	Quantum	data collection
DENZO		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I82

3i82

Resolution: 1.998→59.595 Å / Occupancy max: 1 / Occupancy min: 0.27 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.28 / Stereochemistry target values: MLHL
Details: REFINEMENT WAS CARRIED OUT WITH EXPLICIT HYDROGENS AS DEFINED BY THE RIDING MODEL.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.193	3311	5.08 %	RANDOM
R_work	0.1703	-	-	-
obs	0.1715	65223	98.63 %	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.001 Å² / k_sol: 0.4 e/Å³

Displacement parameters

B_iso max: 105.6 Å² / B_iso mean: 33.5746 Å² / B_iso min: 15.06 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.3459 Å²	0 Å²	-0 Å²
2-	-	2.3459 Å²	-0 Å²
3-	-	-	-4.6918 Å²

Refinement step

Cycle: LAST / Resolution: 1.998→59.595 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4824	0	1	245	5070

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5003
X-RAY DIFFRACTION	f_angle_d	1.058	6827
X-RAY DIFFRACTION	f_chiral_restr	0.065	801
X-RAY DIFFRACTION	f_plane_restr	0.005	901
X-RAY DIFFRACTION	f_dihedral_angle_d	13.036	1809

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.998-2.0266	0.2209	128	0.1879	2490	2618	98
2.0266-2.0569	0.211	130	0.1731	2582	2712	100
2.0569-2.089	0.2044	141	0.1774	2541	2682	100
2.089-2.1233	0.2088	135	0.1672	2604	2739	100
2.1233-2.1599	0.1861	139	0.1635	2545	2684	100
2.1599-2.1992	0.1782	129	0.1615	2582	2711	100
2.1992-2.2415	0.1828	136	0.1594	2560	2696	99
2.2415-2.2872	0.1723	148	0.1601	2579	2727	99
2.2872-2.3369	0.1775	129	0.1544	2564	2693	99
2.3369-2.3913	0.1869	132	0.1609	2552	2684	100
2.3913-2.4511	0.2135	128	0.1624	2580	2708	99
2.4511-2.5174	0.185	144	0.1674	2576	2720	100
2.5174-2.5915	0.1739	167	0.1619	2555	2722	100
2.5915-2.6751	0.1922	133	0.1628	2589	2722	100
2.6751-2.7707	0.1943	133	0.159	2613	2746	100
2.7707-2.8817	0.1852	155	0.1622	2586	2741	100
2.8817-3.0128	0.1879	115	0.1671	2618	2733	99
3.0128-3.1716	0.2106	140	0.168	2597	2737	100
3.1716-3.3703	0.1989	125	0.1811	2637	2762	99
3.3703-3.6305	0.2207	145	0.1782	2608	2753	98
3.6305-3.9958	0.1958	147	0.1705	2562	2709	97
3.9958-4.5738	0.1565	137	0.1534	2551	2688	95
4.5738-5.7618	0.197	156	0.1682	2524	2680	93
5.7618-59.6215	0.2055	139	0.2112	2717	2856	94

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	1.2538	-1.1989	0.6014	3.376	-1.5127	1.6049	0.0811	0.0255	-0.0857	0.0075	-0.1232	-0.6863	0.0606	0.468	0.1746	0.1207	0.0135	-0.0534	0.2919	0.044	0.2888	-29.7694	-2.8977	1.5896
2	7.1649	5.7528	-0.0526	4.6828	0.6121	6.5989	-0.2797	0.3549	-0.4209	0.0657	0.0468	-0.4738	-0.3576	-0.3958	0.1497	0.2234	0.0394	-0.0788	0.2487	-0.072	0.3641	-48.1389	19.1044	-2.7976
3	5.1393	-2.7613	0.4915	2.2079	0.4825	1.7071	-0.3096	-0.3213	0.1105	0.5686	0.081	0.3327	-0.0831	-0.0709	0.1654	0.1847	-0.0239	0.0216	0.2238	-0.002	0.2569	-43.4581	11.8797	2.9649
4	1.9189	-0.3492	-1.1488	2.3553	1.8302	5.38	0.0037	-0.1692	0.1085	0.2333	-0.0414	-0.0106	0.1672	0.1836	0.0478	0.0904	-0.0239	-0.0128	0.1473	0.0069	0.1906	-39.985	1.6293	1.1305
5	0.6269	0.5142	0.7236	6.6365	1.4329	1.5181	-0.017	-0.0966	0.0488	0.5072	-0.0644	-0.3611	-0.0424	0.1467	0.0779	0.1712	-0.0213	0.0006	0.2427	0.0233	0.212	-34.788	4.1582	6.9834
6	4.0989	-0.8439	-1.9853	2.49	0.77	3.5466	-0.005	-0.4265	-0.14	0.371	0.1508	-0.2456	0.2145	0.5565	-0.245	0.1603	0.0083	-0.0671	0.2185	0.0278	0.1843	-36.4899	-11.7749	8.0462
7	5.7544	-0.8909	-0.8031	9.1066	0.3707	7.0517	-0.1315	-0.1497	0.0105	0.0394	-0.2025	0.1426	0.4341	-1.0234	0.2938	0.262	-0.0804	0.0506	0.3135	-0.0924	0.2542	-49.6282	-0.5384	14.6121
8	2.5023	0.4682	-0.6838	2.7385	-0.8179	7.1543	0.1825	-0.2933	-0.1498	0.4515	-0.0653	-0.051	0.2309	-0.0565	-0.085	0.2053	-0.0375	-0.0113	0.1742	0.0184	0.1417	-47.4587	-16.0329	8.9992
9	2.2085	-0.3601	-0.7496	1.9818	0.7057	3.728	0.0338	-0.3463	-0.2282	0.5251	-0.0008	-0.1758	0.2046	0.2851	-0.0389	0.2438	-0.0151	-0.0464	0.1829	0.0373	0.2055	-42.4779	-16.8289	7.76
10	1.665	0.0772	-0.0125	1.6571	1.6949	5.058	0.1726	-0.2504	-0.1752	-0.0778	-0.0509	-0.1658	0.1283	-0.11	-0.2027	0.2495	0.0408	0.0004	0.1731	0.0288	0.227	-48.5348	-25.2494	-6.7792
11	1.7243	0.7457	0.5796	2.4411	-0.1606	1.8885	-0.0072	-0.1982	-0.1133	-0.032	0.0033	0.1068	0.1855	-0.2453	-0.0326	0.1166	0.0306	0.0055	0.1322	0.0131	0.101	-53.1123	-22.6997	-6.3466
12	2.5553	0.7327	-0.6591	4.4723	-1.1006	5.4291	0.1536	-0.3343	-0.451	0.0365	-0.1076	-0.0794	0.6141	-0.2658	-0.0147	0.2052	-0.0224	-0.0557	0.2275	0.0697	0.2536	-54.0221	-32.0337	-4.2673
13	7.5877	2.3419	-0.2032	4.8218	-0.2045	1.1952	-0.2925	0.4407	-0.1908	-0.6199	0.212	-0.2096	0.5134	-0.0868	0.1301	0.3609	0.0304	0.0354	0.1832	-0.0153	0.1609	-48.0594	-23.5806	-25.9772
14	1.3109	1.4014	-0.5545	2.4308	-0.9249	2.7269	-0.0319	0.1308	0.066	-0.348	0.2364	0.3172	0.3911	-0.3134	-0.2148	0.2552	-0.0266	-0.0574	0.1846	0.0367	0.1989	-62.191	-19.4452	-21.9387
15	2.3921	1.1814	2.4942	1.8083	3.6038	7.2258	0.2166	0.0183	-0.0519	-0.4674	-0.0548	0.6453	0.9947	-0.9569	-0.4361	0.3451	-0.073	-0.1325	0.2054	0.1045	0.2275	-65.2905	-15.7595	-23.594
16	2.9882	0.2272	0.1035	1.6614	-0.1862	0.7849	-0.0233	0.1508	-0.0504	-0.1003	0.0965	0.124	0.293	-0.134	-0.0797	0.1768	-0.0208	-0.0065	0.124	0.0327	0.0883	-56.496	-14.2486	-20.3978
17	2.5889	1.0731	-0.3564	1.1661	-1.1772	1.5968	0.0911	0.1542	-0.5132	-0.3379	0.0057	-0.2188	0.7166	-0.0549	-0.0716	0.5064	-0.0283	0.0034	0.2126	-0.0299	0.1227	-55.0432	-17.8408	-34.5013
18	5.4321	2.3415	1.0931	3.5211	0.2058	2.7417	-0.2875	0.2594	-0.0524	-0.4167	0.1202	0.0717	0.0109	0.2384	0.1547	0.2593	0.0351	0.0226	0.1122	0.0516	0.1141	-49.3814	-1.1834	-29.8796
19	2.5891	-0.7893	1.431	1.9973	-0.7096	2.3966	-0.0816	0.1604	0.1911	-0.2166	-0.0682	0.0753	-0.1057	-0.0039	0.1464	0.1825	0.0045	0.0108	0.1373	0.0135	0.1364	-53.1161	1.6636	-29.5446
20	4.3525	-0.5876	-1.8442	1.9026	1.3788	2.3164	-0.264	0.3611	0.3968	-0.2018	-0.1529	-0.2987	-0.3662	0.5487	0.2839	0.2415	-0.0708	-0.0012	0.2641	0.1068	0.2594	-37.8389	11.2648	-23.0755
21	0.1529	-0.0769	-0.7807	4.8753	0.0268	4.0787	-0.2615	0.1747	0.3377	0.0889	-0.4006	0.7524	-0.9838	-0.8015	0.0242	0.3429	0.0916	-0.1886	0.2276	-0.1222	0.4717	-57.6956	16.2243	-23.4407
22	0.6984	0.1185	-0.5702	3.448	-0.9962	2.3888	-0.234	-0.0151	0.1545	0.2723	-0.0967	0.0876	-0.5559	0.3307	0.3172	0.225	-0.0612	-0.0652	0.1742	0.0344	0.2647	-41.6641	14.8939	-11.4928
23	0.8034	0.2736	-1.0174	2.5214	-0.6144	1.3368	0.0815	-0.0552	0.7456	0.2478	-0.4926	0.7427	-0.7915	-0.2276	0.2033	0.37	0.053	-0.1354	0.1972	-0.0664	0.4577	-50.0428	18.3622	-12.7234
24	1.0155	-0.9155	-0.2359	6.6823	-0.3379	1.3846	-0.094	-0.0437	0.3609	-0.46	-0.0597	0.2302	-0.1407	-0.0757	0.1539	0.1836	-0.0117	-0.067	0.1784	0.0017	0.2296	-46.4604	9.0223	-14.0085
25	4.5502	-2.9102	0.6874	6.1221	-1.1515	2.1494	-0.2794	0.3433	0.7763	-0.308	-0.2534	-0.2047	-0.5501	0.4596	0.3335	0.3522	-0.1448	-0.1076	0.261	0.0756	0.316	-37.3376	19.6918	-16.3945
26	3.1876	1.2829	3.4969	1.5371	3.0132	6.3551	0.1307	0.18	-0.0572	-0.0368	0.1843	-0.3592	-0.3609	1.0204	-0.2622	0.1789	-0.081	-0.0447	0.3275	0.0391	0.3383	-25.004	12.1013	4.4116

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 (resseq 1:16)	A	1 - 16
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 17:27)	A	17 - 27
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 28:43)	A	28 - 43
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 44:82)	A	44 - 82
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 83:116)	A	83 - 116
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 117:132)	A	117 - 132
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 133:146)	A	133 - 146
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 147:176)	A	147 - 176
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 177:215)	A	177 - 215
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 1:26)	B	1 - 26
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 27:82)	B	27 - 82
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 83:106)	B	83 - 106
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 107:128)	B	107 - 128
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 129:166)	B	129 - 166
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 167:176)	B	167 - 176
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 177:192)	B	177 - 192
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 193:218)	B	193 - 218
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 1:26)	C	1 - 26
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 27:106)	C	27 - 106
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 107:132)	C	107 - 132
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 133:146)	C	133 - 146
22	X-RAY DIFFRACTION	22	chain 'C' and (resseq 147:166)	C	147 - 166
23	X-RAY DIFFRACTION	23	chain 'C' and (resseq 167:176)	C	167 - 176
24	X-RAY DIFFRACTION	24	chain 'C' and (resseq 177:192)	C	177 - 192
25	X-RAY DIFFRACTION	25	chain 'C' and (resseq 193:212)	C	193 - 212
26	X-RAY DIFFRACTION	26	chain 'C' and (resseq 213:225)	C	213 - 225

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