PDB-5fus: Crystal structure of B. cenocepacia DfsA

ID or keywords:

Entry

Database: PDB / ID: 5fus

Title

Crystal structure of B. cenocepacia DfsA

Components

Putative enoyl CoA hydratase

Enoyl-CoA hydratase

Keywords

LYASE /

CROTONASE /

QUORUM SENSING / BDSF BIOSYNTHESIS

Function / homology

Function and homology information

catalytic activity
Similarity search - Function

Biological species

Burkholderia cenocepacia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.87 Å

Authors

Spadaro, F. / Scoffone, V.C. / Chiarelli, L.R. / Fumagalli, M. / Buroni, S. / Riccardi, G. / Forneris, F.

Citation

Journal: Biochemistry / Year: 2016
Title: The Crystal Structure of Burkholderia Cenocepacia Dfsa Provides Insights Into Substrate Recognition and Quorum Sensing Fatty Acid Biosynthesis.
Authors: Spadaro, F. / Scoffone, V.C. / Chiarelli, L.R. / Fumagalli, M. / Buroni, S. / Riccardi, G. / Forneris, F.

History

Deposition	Jan 29, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 1, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 29, 2016	Group: Database references
Revision 2.0	Jun 30, 2021	Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Source and taxonomy / Structure summary Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_site Item: _atom_site.occupancy / _entity.pdbx_description ..._atom_site.occupancy / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_vector / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _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.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.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1	Jan 10, 2024	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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PDBx/mmCIF format	5fus.cif.gz	337.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5fus.ent.gz	276.9 KB	Display	PDB format
PDBx/mmJSON format	5fus.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fu/5fus ftp://data.pdbj.org/pub/pdb/validation_reports/fu/5fus	HTTPS FTP

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Related structure data

Related structure data	3m6mS S: Starting model for refinement
Similar structure data	2x0f-d 2x0e-d 4at0-1 2x0d-d 4eo3-d 4at2-1 4q3k-1 4mr0-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	#143 - Nov 2011 Toll-like Receptors similarity (1)

Deposited unit

A: Putative enoyl CoA hydratase

B: Putative enoyl CoA hydratase

C: Putative enoyl CoA hydratase

hetero molecules

98 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)	128.070, 128.070, 128.890
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	B-2027- HOH
2	1	B-2073- HOH
3	1	B-2182- HOH
4	1	B-2183- HOH

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Protein , 1 types, 3 molecules ABC

#1: Protein	Putative enoyl CoA hydratase / Enoyl-CoA hydratase Mass: 32035.668 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria) Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610 Gene: BCAM0581 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4EKM5

#1: Protein

Putative enoyl CoA hydratase /

Enoyl-CoA hydratase

Mass: 32035.668 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAM0581 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4EKM5

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Non-polymers , 6 types, 504 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol Mass: 120.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₅H₁₂O₃ / Comment: inhibitor, precipitant*YM
#5: Chemical	ChemComp-DAO / LAURIC ACID / Lauric acid Mass: 200.318 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₂H₂₄O₂
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 487 / 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: 3.4 Å³/Da / Density % sol: 63.8 % / Description: NONE
Crystal grow	Details: 50 MM TRIS-HCL 50 MM LISO4 50 MM NA2SO4 30% PEG 400 PH 8.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873 Å / Relative weight: 1
Reflection	Resolution: 1.9→55.69 Å / Num. obs: 95772 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / B_iso Wilson estimate: 25.07 Å² / R_merge(I) obs: 0.15 / Net I/σ(I): 6.7
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.77 / Mean I/σ(I) obs: 1.8 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M6M

3m6m

Resolution: 1.87→45.424 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 19.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1977	5157	5.1 %
R_work	0.1662	-	-
obs	0.1678	100676	99.77 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.7 Å²

Refinement step

Cycle: LAST / Resolution: 1.87→45.424 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6309	0	124	487	6920

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	6650
X-RAY DIFFRACTION	f_angle_d	1.455	8982
X-RAY DIFFRACTION	f_dihedral_angle_d	14.332	2434
X-RAY DIFFRACTION	f_chiral_restr	0.085	964
X-RAY DIFFRACTION	f_plane_restr	0.007	1158

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 (%)
1.87-1.8913	0.3179	163	0.288	3110	X-RAY DIFFRACTION	99
1.8913-1.9135	0.2999	175	0.2932	3129	X-RAY DIFFRACTION	99
1.9135-1.9369	0.3267	160	0.2806	3141	X-RAY DIFFRACTION	100
1.9369-1.9614	0.2939	140	0.2705	3173	X-RAY DIFFRACTION	100
1.9614-1.9872	0.3004	145	0.255	3188	X-RAY DIFFRACTION	100
1.9872-2.0144	0.2891	166	0.2413	3187	X-RAY DIFFRACTION	100
2.0144-2.0432	0.2711	177	0.2222	3146	X-RAY DIFFRACTION	100
2.0432-2.0737	0.2531	198	0.214	3141	X-RAY DIFFRACTION	100
2.0737-2.1061	0.2536	193	0.2076	3148	X-RAY DIFFRACTION	100
2.1061-2.1406	0.2339	185	0.2022	3156	X-RAY DIFFRACTION	100
2.1406-2.1775	0.2292	181	0.1866	3150	X-RAY DIFFRACTION	100
2.1775-2.2171	0.2316	205	0.1792	3151	X-RAY DIFFRACTION	99
2.2171-2.2598	0.1964	154	0.1661	3119	X-RAY DIFFRACTION	99
2.2598-2.3059	0.2115	153	0.1702	3205	X-RAY DIFFRACTION	100
2.3059-2.356	0.2102	189	0.1601	3172	X-RAY DIFFRACTION	100
2.356-2.4108	0.1856	182	0.158	3143	X-RAY DIFFRACTION	100
2.4108-2.4711	0.2076	149	0.1586	3225	X-RAY DIFFRACTION	100
2.4711-2.5379	0.1954	176	0.1555	3147	X-RAY DIFFRACTION	100
2.5379-2.6126	0.1944	195	0.1543	3180	X-RAY DIFFRACTION	100
2.6126-2.6969	0.1645	182	0.1511	3158	X-RAY DIFFRACTION	100
2.6969-2.7933	0.2062	166	0.1468	3213	X-RAY DIFFRACTION	100
2.7933-2.9051	0.1641	169	0.1437	3177	X-RAY DIFFRACTION	100
2.9051-3.0373	0.1765	161	0.1428	3213	X-RAY DIFFRACTION	100
3.0373-3.1974	0.1641	171	0.1444	3195	X-RAY DIFFRACTION	100
3.1974-3.3977	0.1478	153	0.1418	3204	X-RAY DIFFRACTION	100
3.3977-3.6599	0.1929	158	0.1396	3255	X-RAY DIFFRACTION	100
3.6599-4.028	0.1829	134	0.1418	3257	X-RAY DIFFRACTION	100
4.028-4.6104	0.1562	193	0.1406	3210	X-RAY DIFFRACTION	100
4.6104-5.8067	0.1737	179	0.1646	3267	X-RAY DIFFRACTION	100
5.8067-45.4372	0.208	205	0.1802	3359	X-RAY DIFFRACTION	99

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	0.6857	0.54	0.0388	0.9544	-0.3584	0.5884	0.2149	-0.1231	0.0732	0.7237	-0.0865	-0.1917	0.083	0.0337	0.2287	0.5073	-0.0012	-0.0774	0.4017	-0.0111	0.2118	102.9859	35.6722	59.6506
2	0.7037	-0.5682	0.1835	1.0708	-0.0479	0.2099	-0.0356	-0.1658	0.0754	0.1588	0.0431	-0.0318	-0.0045	-0.0322	0	0.153	0.0069	0.0202	0.2214	-0.007	0.108	94.8373	41.4285	46.8532
3	0.3152	-0.3022	-0.0197	0.7751	0.3255	0.2011	-0.003	-0.0712	-0.0693	0.0809	0.0183	0.0614	0.0557	-0.0269	0	0.1405	-0.0022	0.0098	0.1751	0.0282	0.1343	93.7087	31.9574	43.3141
4	0.1565	0.1309	-0.0681	0.4489	-0.2339	0.4503	-0.0792	-0.3297	0.0528	0.2429	-0.0535	0.0037	0.1067	0.0472	-0.0316	0.2354	0.042	0.0579	0.3584	-0.0667	0.2216	81.4443	59.0989	50.1002
5	0.0563	0.0382	-0.0088	0.0117	0.0138	0.0943	0.0601	0.2687	0.4787	-0.1362	-0.0161	0.1368	-0.5591	-0.2682	-0.0025	0.3973	0.1389	0.0214	0.3245	0.0278	0.342	72.8459	61.8367	11.6937
6	0.7278	0.1303	-0.3882	0.2636	-0.2769	0.2727	-0.0963	0.559	-0.1745	-0.3839	0.0042	0.2423	-0.3028	-0.2995	-0.009	0.2703	0.0551	-0.0234	0.3841	-0.055	0.291	71.7829	52.9021	11.7781
7	0.1784	-0.2108	0.0552	0.2318	-0.1198	0.2072	0.1556	0.0614	0.0853	-0.0907	-0.1591	-0.1282	-0.2916	-0.1072	0	0.2531	0.0043	0.0353	0.2253	0.0181	0.2314	80.6914	57.1344	13.4198
8	-0.0317	-0.0336	0.0005	0.0457	0.178	0.037	0.0061	0.1942	0.1065	-0.271	-0.0045	0.202	-0.1852	-0.2668	-0.0001	0.3127	-0.0116	-0.0656	0.3136	0.0045	0.2494	76.7583	40.809	-1.0948
9	0.1259	-0.0979	-0.0125	0.1191	0.0353	0.0516	-0.0581	-0.0312	0.1162	-0.1361	0.2037	0.0084	-0.1714	0.1452	0.0084	0.208	-0.0279	-0.0244	0.1838	-0.0013	0.22	88.499	44.7511	5.8766
10	0.5426	-0.0856	-0.1805	0.3323	0.4072	0.549	0.0126	-0.0511	-0.0569	-0.0372	-0.0613	0.1128	0.0287	-0.1315	-0	0.138	-0.0106	-0.0062	0.2051	-0.0058	0.1861	75.749	37.1014	17.3142
11	0.1136	-0.004	0.159	0.1026	-0.0465	0.1738	0.0426	-0.0542	0.0559	-0.0079	-0.0359	-0.0079	-0.0177	-0.0954	0.0148	0.1317	0.0282	0.0153	0.2188	-0.0408	0.1657	78.0012	50.0968	29.5516
12	0.0622	-0.0651	0.0486	0.0434	-0.0539	0.0452	-0.0105	0.0036	-0.1163	-0.1027	0.1765	-0.2088	-0.1774	0.1708	0.0002	0.1764	-0.0242	-0.0178	0.1841	-0.0068	0.1674	92.0712	37.4933	8.0242
13	-0.0024	-0.0101	-0.0325	0.0386	-0.0256	0.049	0.0674	-0.1575	-0.0712	0.1767	-0.0256	-0.0451	0.0777	-0.1553	-0.0007	0.2015	-0.0326	-0.0461	0.2563	-0.0301	0.222	75.2321	30.3866	-6.4841
14	0.41	-0.2924	0.0483	0.4432	0.3748	0.1889	0.2093	0.2291	-0.3686	-0.1297	-0.08	-0.2137	0.2315	0.1653	0.0009	0.2452	0.0264	-0.0312	0.2182	-0.0628	0.3277	103.0338	6.5481	8.0629
15	0.6749	-0.0528	0.2909	0.3177	-0.3478	0.8607	0.0425	-0.0395	-0.1433	-0.0301	0.0076	0.0012	0.1423	-0.0375	0.0011	0.1848	-0.025	-0.0225	0.1352	0.0221	0.2139	98.1045	12.474	23.554
16	0.3132	-0.2475	0.1321	0.1362	0.0918	0.306	0.0771	0.0491	-0.0528	-0.017	0.0641	-0.0404	0.0485	-0.0632	0.1926	0.1907	-0.0309	-0.0479	0.1776	0.0004	0.1962	87.6275	19.0333	8.8078
17	0.3136	-0.3227	-0.0294	0.1737	-0.0175	0.2339	-0.0471	-0.0581	0.0031	-0.0801	-0.0407	-0.1746	0.1497	-0.006	-0.0258	0.2073	-0.011	-0.0279	0.1511	0.0433	0.2076	108.7571	13.1825	33.208

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'C' AND (RESID 9 THROUGH 45 )
2	X-RAY DIFFRACTION	2	CHAIN 'C' AND (RESID 46 THROUGH 188 )
3	X-RAY DIFFRACTION	3	CHAIN 'C' AND (RESID 189 THROUGH 261 )
4	X-RAY DIFFRACTION	4	CHAIN 'C' AND (RESID 262 THROUGH 278 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 9 THROUGH 26 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 27 THROUGH 45 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 46 THROUGH 73 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 74 THROUGH 96 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 97 THROUGH 115 )
10	X-RAY DIFFRACTION	10	CHAIN 'A' AND (RESID 116 THROUGH 211 )
11	X-RAY DIFFRACTION	11	CHAIN 'A' AND (RESID 212 THROUGH 241 )
12	X-RAY DIFFRACTION	12	CHAIN 'A' AND (RESID 242 THROUGH 261 )
13	X-RAY DIFFRACTION	13	CHAIN 'A' AND (RESID 262 THROUGH 277 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 7 THROUGH 61 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 62 THROUGH 211 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 212 THROUGH 241 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 242 THROUGH 278 )

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Protein , 1 types, 3 molecules ABC

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Non-polymers , 6 types, 504 molecules

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Movie

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Structure viewers

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Viewer log

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This page

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Open data

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Download

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Validation report

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Links

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Assembly

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Components

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Protein , 1 types, 3 molecules ABC

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Non-polymers , 6 types, 504 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi