PDB-4fdz: EutL from Clostridium perfringens, Crystallized Under Reducing Co...

ID or keywords:

Entry

Database: PDB / ID: 4fdz

Title

EutL from Clostridium perfringens, Crystallized Under Reducing Conditions

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 / Resolution: 1.802 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	May 29, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 29, 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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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PDBx/mmCIF format	4fdz.cif.gz	374.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4fdz.ent.gz	315 KB	Display	PDB format
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Validation report

Summary document	4fdz_validation.pdf.gz	429.1 KB	Display	wwPDB validaton report
Full document	4fdz_full_validation.pdf.gz	430.2 KB	Display
Data in XML	4fdz_validation.xml.gz	30.4 KB	Display
Data in CIF	4fdz_validation.cif.gz	45.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fd/4fdz ftp://data.pdbj.org/pub/pdb/validation_reports/fd/4fdz	HTTPS FTP

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Related structure data

Related structure data	4ediSC 4tm6C 4tmeC 4fe0 PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4tme-d 6ard-d 4tm6-d 6arc-d 4tlh-d 4u6i-d 3gfh-1 4edi-d 5djb-2 6nlu-1 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)	87.970, 87.970, 252.460
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 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.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 619 / 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: 3.43 Å³/Da / Density % sol: 64.16 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES buffer, 5% PEG 8000, 8% ethylene glycol, 5mM tris(2-carboxyethyl)phosphine, 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: 0.97918 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.8→19.824 Å / Num. obs: 91132 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.67 % / B_iso Wilson estimate: 19.78 Å² / R_merge(I) obs: 0.055 / Net I/σ(I): 18.42

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.8-1.85		0.393	3.87	28100	6364	95
1.85-1.9		0.325	4.81	29738	6471	98.7
1.9-1.95		0.257	6.1	29523	6324	98.7
1.95-2.01		0.206	7.57	28802	6112	99
2.01-2.08		0.159	9.43	28278	5964	99
2.08-2.15		0.13	11.39	27641	5794	99.1
2.15-2.24		0.109	13.29	26840	5580	99.2
2.24-2.33		0.097	14.76	25879	5387	99.3
2.33-2.43		0.083	16.83	24951	5194	99.3
2.43-2.55		0.071	19.2	23765	4961	99.5
2.55-2.69		0.059	22.6	22727	4750	99.5
2.69-2.85		0.052	25.27	21476	4522	99.6
2.85-3.05		0.046	28.44	19863	4223	99.4
3.05-3.29		0.041	31.36	18301	3964	99.6
3.29-3.6		0.035	35.55	16547	3641	98.9
3.6-4.03		0.032	38.08	14823	3331	98.8
4.03-4.65		0.029	41.53	13670	2950	98.9
4.65-5.7		0.028	42.1	11584	2534	98.8
5.7-8.06		0.029	41.39	8941	1996	98.3
	8.06	0.028	42.14	4308	1070	87.9

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.11	data extraction
ADSC	Quantum	data collection
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4EDI

4edi

Resolution: 1.802→19.824 Å / Occupancy max: 1 / Occupancy min: 0.05 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 15.03 / Stereochemistry target values: ML
Details: REFINEMENT WAS CARRIED OUT WITH EXPLICIT HYDROGENS AS DEFINED BY THE RIDING MODEL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1773	4634	5.08 %	RANDOM
R_work	0.16	-	-	-
obs	0.1609	91131	98.77 %	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 34.198 Å² / k_sol: 0.355 e/Å³

Displacement parameters

B_iso max: 87.72 Å² / B_iso mean: 22.8876 Å² / B_iso min: 8.27 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.3752 Å²	0 Å²	-0 Å²
2-	-	4.3752 Å²	-0 Å²
3-	-	-	-1.091 Å²

Refinement step

Cycle: LAST / Resolution: 1.802→19.824 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4864	0	3	619	5486

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5137
X-RAY DIFFRACTION	f_angle_d	1.03	7037
X-RAY DIFFRACTION	f_chiral_restr	0.065	826
X-RAY DIFFRACTION	f_plane_restr	0.005	929
X-RAY DIFFRACTION	f_dihedral_angle_d	12.694	1882

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8022-1.8227	0.2626	138	0.2152	2587	2725	91
1.8227-1.8441	0.2261	154	0.1933	2838	2992	98
1.8441-1.8666	0.2227	152	0.1911	2821	2973	99
1.8666-1.8902	0.2142	152	0.184	2847	2999	99
1.8902-1.9151	0.1902	152	0.1755	2851	3003	99
1.9151-1.9413	0.2071	152	0.1672	2816	2968	99
1.9413-1.969	0.2063	154	0.1699	2848	3002	99
1.969-1.9984	0.1866	152	0.1665	2879	3031	99
1.9984-2.0296	0.185	139	0.1569	2821	2960	99
2.0296-2.0628	0.1718	152	0.153	2861	3013	99
2.0628-2.0983	0.1788	155	0.1539	2886	3041	99
2.0983-2.1364	0.1661	152	0.1512	2853	3005	99
2.1364-2.1775	0.1756	156	0.1448	2841	2997	99
2.1775-2.2219	0.1606	158	0.143	2876	3034	99
2.2219-2.2701	0.1613	145	0.1437	2880	3025	99
2.2701-2.3228	0.1617	156	0.1416	2864	3020	99
2.3228-2.3808	0.1552	152	0.1405	2898	3050	99
2.3808-2.4451	0.1704	147	0.1468	2902	3049	99
2.4451-2.5169	0.1704	146	0.1547	2908	3054	100
2.5169-2.598	0.1704	188	0.1505	2854	3042	99
2.598-2.6906	0.1772	153	0.1508	2881	3034	99
2.6906-2.7981	0.1758	150	0.154	2918	3068	100
2.7981-2.925	0.1806	168	0.1636	2913	3081	99
2.925-3.0787	0.1781	140	0.1583	2936	3076	100
3.0787-3.2708	0.209	160	0.1667	2959	3119	100
3.2708-3.5221	0.1628	134	0.1634	2949	3083	99
3.5221-3.8741	0.1931	187	0.1651	2893	3080	99
3.8741-4.4292	0.1443	152	0.1522	2977	3129	99
4.4292-5.5599	0.1566	164	0.1487	3009	3173	99
5.5599-19.8253	0.1897	174	0.1915	3131	3305	98

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	1.3025	-1.2791	0.4822	4.0812	-0.2525	1.0191	0.1087	-0.1114	-0.0953	-0.0143	-0.0762	-0.0493	-0.0373	0.0415	0.0032	0.0796	-0.0488	-0.0343	0.161	0.0203	0.1281	-37.8	5.4496	-0.3136
2	1.1408	0.5999	0.3294	4.5748	0.2443	0.4951	-0.0639	-0.236	0.1568	0.3086	0.0049	0.2458	0.06	-0.0993	0.0614	0.1116	-0.0358	-0.007	0.1928	0.005	0.0956	-44.124	11.9794	2.782
3	0.7326	0.2109	-0.1663	1.0745	0.3556	1.5522	0.1263	-0.1607	-0.0129	0.1229	-0.1427	-0.0193	-0.0435	0.009	-0.0003	0.1073	-0.0748	-0.0095	0.1315	0.0125	0.1154	-40.7274	1.5622	1.4254
4	0.6685	0.6135	0.4933	2.5724	0.36	0.5735	0.1626	-0.0951	-0.1156	0.3519	-0.1262	-0.3126	0.0647	0.0619	-0.038	0.1366	-0.0692	-0.0321	0.1932	0.0308	0.1511	-35.4867	-1.832	6.4382
5	5.4439	-1.358	-1.4497	4.9265	-0.7977	0.6806	0.0765	-0.3324	0.0055	0.2413	-0.0417	0.3676	0.2753	-0.5337	-0.0653	0.2251	-0.1232	0.0218	0.2614	-0.0277	0.13	-49.0715	0.0055	15.6165
6	0.3541	-0.2005	0.0392	0.1632	-0.2036	1.1527	0.1744	-0.1957	-0.0915	0.2968	-0.1236	0.0334	0.1139	-0.0703	-0.0555	0.2185	-0.1033	-0.0145	0.1668	0.0295	0.1139	-48.291	-14.1088	7.6926
7	1.2416	-0.8434	-1.6419	1.9036	1.9351	4.413	0.0318	-0.4043	-0.1652	0.4467	0.0906	-0.2078	0.2854	0.4913	0.0463	0.2711	-0.0756	-0.1181	0.2206	0.0978	0.216	-40.8066	-21.0388	10.9671
8	0.6785	0.1562	-0.118	0.4723	-0.4862	6.8816	0.072	0.0267	-0.1788	-0.3063	-0.0846	-0.2238	0.4201	0.0775	-0.0406	0.292	0.019	0.0345	0.0762	0.0058	0.1894	-45.4783	-27.7435	-15.8588
9	4.478	-1.9829	2.8476	4.8229	-1.5895	4.7715	0.2869	-0.639	0.11	0.2712	-0.3202	-0.073	0.1257	-0.2398	0.0343	0.21	-0.1626	-0.0032	0.4304	-0.0076	0.1676	-57.509	-20.6204	10.1319
10	0.9662	0.6878	0.272	1.9098	-0.1075	1.0259	0.0756	-0.1709	-0.0645	0.0007	-0.0995	0.0331	0.1047	-0.1054	0.0298	0.1004	-0.0224	-0.0254	0.0881	0.021	0.0808	-54.4275	-22.896	-6.1572
11	0.5273	0.0029	-0.7962	0.3223	0.0715	1.2376	0.0126	-0.2815	-0.3047	0.0529	-0.1294	-0.0781	0.3412	0.0752	0.1423	0.1672	-0.0418	-0.0208	0.1246	0.0639	0.1437	-55.4314	-31.9587	-4.1715
12	4.4533	1.8903	-1.4532	6.4908	0.2497	1.5489	0.0293	-0.2254	-0.227	-0.0427	-0.3226	-0.4448	0.3877	0.1837	0.2379	0.2531	-0.0022	0.0448	0.0933	-0.0101	0.1942	-48.5607	-26.6451	-24.2304
13	2.3001	0.2095	1.1481	2.787	0.38	0.9478	-0.0837	0.2648	-0.3973	-0.3867	0.0326	-0.4349	0.3074	0.0006	0.1446	0.2251	-0.0021	0.0167	0.0439	-0.0046	0.1261	-49.6139	-22.2198	-26.7422
14	3.4606	0.4455	-0.1685	4.7145	-0.3596	0.844	0.0849	-0.0333	-0.024	-0.113	-0.0316	0.2769	0.2181	-0.3342	-0.0149	0.2066	-0.0863	-0.0444	0.1455	0.0404	0.1244	-68.9737	-25.347	-14.6944
15	0.9449	0.6075	0.2747	1.0296	0.6381	0.4118	-0.05	0.0528	0.0381	-0.3516	0.1075	0.1839	0.1623	-0.0837	-0.0509	0.2155	-0.0417	-0.0482	0.0846	0.0187	0.1164	-59.2537	-15.2048	-28.1442
16	2.0682	1.7795	1.2446	1.9213	1.5183	1.2686	-0.0581	-0.1297	0.08	-0.2157	-0.0411	0.2254	0.1736	-0.2753	0.0486	0.1653	-0.0573	-0.0394	0.083	0.0334	0.1228	-61.4154	-15.1951	-21.522
17	0.3067	0.1735	-0.258	0.8902	-0.2527	0.6161	-0.0056	0.0562	-0.1193	-0.2981	0.0747	0.0646	0.3112	-0.0823	0.0813	0.3654	-0.0522	-0.0351	0.0229	-0.0388	0.064	-55.92	-17.3759	-34.9851
18	0.7609	0.0678	0.3078	1.447	0.0454	1.3995	-0.0168	0.1352	0.0966	-0.3521	-0.0121	0.1737	-0.0542	-0.004	0.0419	0.1829	0.0003	-0.0266	0.0498	0.0086	0.0969	-54.6302	-1.5265	-30.1065
19	0.9743	-0.1726	0.2796	1.133	-0.3732	1.2645	0.0218	0.0721	0.053	-0.2944	-0.0409	0.0426	-0.0578	-0.0161	0.0206	0.1689	0.0047	-0.0106	0.062	-0.0061	0.093	-52.0648	2.0775	-29.4686
20	0.5474	0.0137	-1.0917	3.0709	-1.5068	2.8862	-0.0988	0.1187	-0.0769	-0.4767	0.0634	-0.1115	0.1867	0.3486	0.0407	0.1984	-0.077	0.0312	0.1645	0.0281	0.1238	-36.931	8.5544	-26.899
21	1.1498	0.0148	0.312	1.6624	0.1054	1.7771	-0.0506	0.0904	0.1742	-0.1551	-0.1436	0.0359	-0.3058	0.0941	0.1251	0.1731	-0.0232	-0.0235	0.0734	0.0036	0.1185	-45.4614	14.364	-18.4635
22	1.1295	0.7857	-0.2719	4.0872	-1.3024	0.5455	-0.0524	-0.1606	0.2451	0.0814	-0.0642	0.3046	-0.2914	-0.0798	0.1046	0.2107	0.008	-0.0399	0.1242	-0.0372	0.133	-48.6628	12.6409	-13.7015
23	0.3695	-0.039	0.1533	0.9845	-0.1641	0.4485	-0.1154	0.0664	0.2237	-0.0891	-0.0618	0.0097	-0.2304	0.1705	-0.057	0.272	-0.1721	-0.0553	0.1135	0.0596	0.2093	-37.4903	19.4105	-16.7427
24	0.6942	0.4248	0.5904	0.6317	0.4845	1.3958	0.0351	0.0469	-0.0442	0.0124	0.0328	-0.188	-0.0392	0.1414	0.03	0.1301	-0.186	-0.0529	0.2225	0.0495	0.1968	-25.3865	12.0418	4.2791

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 1:26)	A	1 - 26
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 27:43)	A	27 - 43
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 44:82)	A	44 - 82
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 83:128)	A	83 - 128
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 129:145)	A	129 - 145
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 146:192)	A	146 - 192
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 193:215)	A	193 - 215
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 1:16)	B	1 - 16
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 17:26)	B	17 - 26
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 27:82)	B	27 - 82
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 83:106)	B	83 - 106
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 107:116)	B	107 - 116
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 117:128)	B	117 - 128
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 129:145)	B	129 - 145
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 146:167)	B	146 - 167
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 168:192)	B	168 - 192
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 193:219)	B	193 - 219
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 1:43)	C	1 - 43
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 44:106)	C	44 - 106
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 107:116)	C	107 - 116
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 117:167)	C	117 - 167
22	X-RAY DIFFRACTION	22	chain 'C' and (resseq 168:192)	C	168 - 192
23	X-RAY DIFFRACTION	23	chain 'C' and (resseq 193:212)	C	193 - 212
24	X-RAY DIFFRACTION	24	chain 'C' and (resseq 213:225)	C	213 - 225

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