PDB-5ez3: Crystal structure Acyl-CoA dehydrogenase from Brucella melitensis...

ID or keywords:

Entry

Database: PDB / ID: 5ez3

Title

Crystal structure Acyl-CoA dehydrogenase from Brucella melitensis in complex with FAD

Components

Acyl-CoA dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / dehydrogenase / FAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Brucella melitensis biotype 1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.15 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure Acyl-CoA dehydrogenase from Brucella melitensis in complex with FAD
Authors: Abendroth, J. / Sankaran, B. / Lorimer, D. / Edwards, T.

History

Deposition	Nov 26, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 9, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 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_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ez3.cif.gz	871.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5ez3.ent.gz	715 KB	Display	PDB format
PDBx/mmJSON format	5ez3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ez3_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	5ez3_full_validation.pdf.gz	1.6 MB	Display
Data in XML	5ez3_validation.xml.gz	84.2 KB	Display
Data in CIF	5ez3_validation.cif.gz	122.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ez/5ez3 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/5ez3	HTTPS FTP

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Related structure data

Related structure data	3djlS S: Starting model for refinement
Similar structure data	4tri-d 4uoj-1 5uqc-d 6bop-1 4lv9-d 5cyf-d 6pbj-d 2wya-2 4g47-2 5e4n-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: BrmeA.01048.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#133 - Jan 2011 Nitric Oxide Synthase similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

A: Acyl-CoA dehydrogenase

B: Acyl-CoA dehydrogenase

C: Acyl-CoA dehydrogenase

D: Acyl-CoA dehydrogenase

hetero molecules

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

1

A: Acyl-CoA dehydrogenase

B: Acyl-CoA dehydrogenase

hetero molecules

defined by author&software
128 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Acyl-CoA dehydrogenase

D: Acyl-CoA dehydrogenase

hetero molecules

defined by author&software
128 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.920, 141.250, 193.220
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Acyl-CoA dehydrogenase Mass: 62750.555 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis biotype 1 (bacteria) Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEII0671 / Plasmid: BrmeA.0.1048a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8YC61, Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor

#1: Protein

Acyl-CoA dehydrogenase

Mass: 62750.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Brucella melitensis biotype 1 (bacteria)
Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEII0671 / Plasmid: BrmeA.0.1048a.A1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8YC61, Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor

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Non-polymers , 5 types, 1296 molecules

#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Chemical	ChemComp-CAC / CACODYLATE ION / dimethylarsinate Mass: 136.989 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆AsO₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1277 / 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: 2.63 Å³/Da / Density % sol: 53.31 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: JCSG+ B5: 40% MPD, 5% PEG 8000, 100mM Na-cacodylate/HCl pH 6.5, BrmeA.01048.a.A1.PS01389 at 22.4 mg/ml; cryo: 20% EG; tray 231351b5; puck lwt7-15

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.2 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2012

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.15→50 Å / Num. all: 144369 / Num. obs: 143067 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.34 % / B_iso Wilson estimate: 26.84 Å² / R_merge F obs: 0.997 / R_merge(I) obs: 0.088 / R_rim(I) all: 0.093 / Χ²: 1.046 / Net I/σ(I): 11.23 / Num. measured all: 566602

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.15-2.21		2.91	0.852	0.511	2.11	31706	9228	9127	0.462	97.2
2.31-2.37			0.88	0.351	3.45	31945	8992	8892	0.411	98.9
2.37-2.44			0.908	0.302	4.08	32412	8758	8687	0.352	99.2
2.44-2.52			0.935	0.258	4.93	32560	8499	8437	0.299	99.3
2.52-2.6			0.952	0.226	5.7	32644	8261	8193	0.26	99.2
2.6-2.69			0.96	0.2	6.66	32944	8011	7960	0.229	99.4
2.69-2.79			0.969	0.182	7.43	33173	7698	7645	0.207	99.3
2.79-2.9			0.977	0.154	9.04	33220	7434	7410	0.174	99.7
2.9-3.03			0.983	0.133	10.68	33261	7161	7134	0.15	99.6
3.03-3.18			0.988	0.112	12.76	33089	6829	6818	0.126	99.8
3.18-3.35			0.991	0.093	15.58	32622	6536	6526	0.104	99.8
3.35-3.56			0.995	0.08	18.37	31920	6150	6143	0.089	99.9
3.56-3.8			0.995	0.07	21.62	31263	5842	5838	0.077	99.9
3.8-4.11			0.996	0.061	23.91	29041	5387	5380	0.068	99.9
4.11-4.5			0.997	0.055	26.04	27013	5024	5022	0.061	100
4.5-5.03			0.997	0.051	26.6	24565	4548	4542	0.056	99.9
5.03-5.81			0.998	0.05	25.05	21792	4035	4025	0.056	99.8
5.81-7.12			0.998	0.046	25.54	19155	3462	3455	0.05	99.8
7.12-10.06			0.999	0.032	30.86	15078	2711	2699	0.035	99.6
	10.06		0.999	0.027	32.46	7199	1574	1333	0.03	84.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3.5 Å	19.75 Å
Translation	3.5 Å	19.75 Å

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Processing

Software

Name	Classification
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3djl

3djl

Resolution: 2.15→19.755 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.63 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1785	2000	1.4 %	Random selection
R_work	0.1453	141058	-	-
obs	0.1457	143058	99.24 %	-

Solvent computation

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

Displacement parameters

B_iso max: 100.37 Å² / B_iso mean: 32.0608 Å² / B_iso min: 10.56 Å²

Refinement step

Cycle: final / Resolution: 2.15→19.755 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16348	0	310	1278	17936
B_iso mean	-	-	41.68	35.4	-
Num. residues	-	-	-	-	2163

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	17259
X-RAY DIFFRACTION	f_angle_d	0.891	23496
X-RAY DIFFRACTION	f_chiral_restr	0.048	2593
X-RAY DIFFRACTION	f_plane_restr	0.005	3205
X-RAY DIFFRACTION	f_dihedral_angle_d	12.471	10410

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 (%)
2.15-2.2037	0.2332	138	0.2033	9764	X-RAY DIFFRACTION	97
2.2037-2.2632	0.2273	141	0.1925	9873	X-RAY DIFFRACTION	98
2.2632-2.3297	0.2452	141	0.1824	9939	X-RAY DIFFRACTION	99
2.3297-2.4048	0.2255	140	0.1778	9956	X-RAY DIFFRACTION	99
2.4048-2.4906	0.1907	142	0.1618	10012	X-RAY DIFFRACTION	99
2.4906-2.5901	0.1824	142	0.1563	9965	X-RAY DIFFRACTION	99
2.5901-2.7077	0.1983	142	0.1528	10059	X-RAY DIFFRACTION	99
2.7077-2.8501	0.2155	143	0.1603	10071	X-RAY DIFFRACTION	99
2.8501-3.028	0.2001	142	0.1598	10074	X-RAY DIFFRACTION	100
3.028-3.2609	0.2018	144	0.1515	10111	X-RAY DIFFRACTION	100
3.2609-3.5873	0.1837	145	0.1383	10192	X-RAY DIFFRACTION	100
3.5873-4.1023	0.1547	144	0.1217	10202	X-RAY DIFFRACTION	100
4.1023-5.1532	0.1288	146	0.115	10281	X-RAY DIFFRACTION	100
5.1532-50	0.15	150	0.1315	10559	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	0.8274	0.1279	-0.1455	1.0886	-0.2514	1.0015	-0.0061	-0.3172	-0.3119	0.2036	-0.0068	-0.2477	0.0652	0.2335	-0.0201	0.1933	0.0343	-0.032	0.3201	0.1165	0.3254	31.3747	44.6015	-6.9521
2	1.0742	0.0656	0.0276	1.1483	-0.3416	1.5015	-0.0332	-0.0135	-0.381	-0.1329	-0.024	-0.0377	0.2126	-0.0101	0.0667	0.1531	0.0073	0.0231	0.1254	0.0016	0.2843	23.1391	41.0376	-26.221
3	3.0432	-1.5723	0.053	2.5006	0.129	1.0656	0.0363	0.3091	-0.3118	-0.3105	-0.0661	0.1767	0.101	-0.0954	0.0492	0.1922	-0.0387	-0.0016	0.1623	-0.0165	0.1814	12.3347	50.5634	-35.8843
4	1.8931	0.673	0.4714	1.69	0.5461	2.607	-0.0246	0.269	-0.2275	-0.2593	0.0573	0.0911	0.0487	-0.0649	-0.0197	0.1549	0.0275	-0.0132	0.1328	-0.0182	0.1597	13.8283	51.1499	-35.1642
5	1.2249	-0.1167	-0.4412	1.0852	-0.1792	0.8769	0.0582	-0.36	-0.2947	0.1818	-0.0515	-0.0578	0.0823	-0.0824	-0.0334	0.1607	0.0052	0.0065	0.2538	0.1287	0.2239	16.079	47.9576	-2.7235
6	0.6931	0.2116	-0.2261	2.2957	-0.3888	1.3264	0.042	-0.2098	-0.3147	-0.0449	-0.0201	0.2638	0.1435	-0.2717	-0.0099	0.1612	-0.0124	-0.0007	0.2843	0.0788	0.2481	2.7838	46.9002	-6.7403
7	0.8474	-0.134	0.1621	1.7166	-0.2756	0.1064	-0.0188	-0.4069	-0.2413	0.4468	-0.0025	-0.008	-0.0118	-0.0375	0.0212	0.2294	-0.0146	0.0125	0.4015	0.1299	0.2123	11.528	48.1938	4.0765
8	1.6121	0.1883	0.0793	0.9605	0.3186	0.9992	0.0358	-0.3561	0.2865	0.1036	0.0459	-0.1373	-0.2109	0.1567	-0.06	0.2472	-0.0059	0.0237	0.2633	-0.0633	0.2192	23.3121	81.2079	-2.1852
9	1.3912	-0.2595	0.2447	1.9317	0.4781	1.8321	-0.0188	-0.5898	0.0797	0.4705	0.0151	0.0789	-0.0997	-0.1184	-0.0118	0.2688	-0.0141	0.0387	0.3923	0.0001	0.1569	8.7686	69.4373	7.6148
10	2.2117	-1.701	0.8551	3.903	0.5777	1.4017	-0.0328	-0.3109	-0.1966	0.1952	0.0139	0.4427	0.0436	-0.3067	0.0522	0.122	-0.0141	0.0399	0.3129	0.0164	0.1586	-3.8527	65.4516	-3.9325
11	1.1218	0.1171	-0.1286	0.7773	-0.1258	1.1277	0.0252	-0.2514	0.2987	0.2218	-0.0347	-0.1464	-0.1969	0.0703	0.0133	0.2695	-0.0027	0.0108	0.1652	-0.0441	0.2756	47.4061	93.8073	-27.8409
12	0.8691	0.3515	-0.2716	1.3514	-0.3531	0.6128	0.0586	0.1165	0.3117	0.0138	0.0587	0.1581	-0.1476	-0.0986	-0.1065	0.2236	0.0108	0.0388	0.1443	0.0485	0.2326	30.5331	92.0788	-40.6682
13	2.1148	-1.3792	-0.8129	2.8732	0.8935	1.5942	0.1186	0.373	0.0667	-0.2024	-0.0288	0.2147	-0.0275	-0.2662	-0.1149	0.2101	-0.0347	-0.0142	0.2401	0.0837	0.1829	25.6037	78.816	-51.0592
14	1.2738	0.0597	-0.1419	0.6292	-0.093	0.5002	0.0136	0.1484	0.1409	-0.0617	0.0316	-0.0362	-0.1095	-0.0467	-0.034	0.2241	-0.0046	0.0343	0.1049	0.0248	0.1513	44.8073	85.3202	-44.1403
15	1.7851	0.6463	-0.7653	2.38	-0.7483	1.5052	-0.0659	0.3575	0.1941	-0.4503	0.086	0.0652	0.0875	-0.0723	-0.024	0.2506	0.0003	0.0106	0.1814	0.054	0.1992	55.0377	86.7573	-54.7554
16	0.8063	0.1104	1.0084	4.8654	0.2533	1.7116	0.02	0.0815	0.3119	-0.0306	-0.0381	-0.6096	-0.1884	0.3504	0.0162	0.2048	-0.0584	0.0463	0.1706	0.0397	0.3271	68.3072	91.6608	-42.1506
17	1.0303	-0.0422	0.25	0.5647	0.0279	0.9868	-0.0135	-0.1016	-0.2279	0.0076	0.0064	0.013	0.1601	-0.0595	0.0072	0.1808	-0.0147	0.0269	0.1086	0.0183	0.2371	56.9115	52.2853	-29.1775
18	2.462	1.0366	0.5788	4.6038	0.4755	1.9038	-0.0733	-0.3058	0.0877	0.0062	0.1127	-0.1323	-0.0881	0.1425	-0.0301	0.1559	0.067	0.0593	0.3045	0.0304	0.2089	64.3252	64.5228	-10.6168
19	0.9254	-0.111	0.3008	0.3751	-0.0056	1.0133	-0.025	-0.0878	-0.0976	-0.0324	0.0567	-0.073	-0.0044	0.0375	-0.0299	0.1687	-0.0145	0.0284	0.0907	0.014	0.1921	61.7811	63.4878	-29.5865
20	2.5604	-0.3062	0.3596	1.4203	0.0537	1.1193	-0.0324	-0.0666	0.0087	0.0413	0.0177	-0.3426	-0.0267	0.2017	0.0083	0.1902	-0.0234	0.0373	0.1231	0.022	0.2091	70.982	69.8673	-39.5008
21	1.6613	-1.0991	0.5536	2.8572	0.8697	2.7162	0.0167	0.4279	0.0046	-0.5812	0.0165	-0.3301	-0.034	0.2348	-0.021	0.2632	-0.0246	0.0918	0.2274	-0.007	0.159	65.1232	67.4312	-55.9849

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 77 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 78 through 179 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 180 through 231 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 232 through 299 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 300 through 414 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 415 through 509 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 510 through 551 )	A
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 12 through 372 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 373 through 523 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 524 through 552 )	B
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 12 through 77 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 78 through 179 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 180 through 231 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 232 through 414 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 415 through 509 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 510 through 552 )	C
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 12 through 179 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 180 through 231 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 232 through 375 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 376 through 509 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 510 through 552 )	D

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Protein , 1 types, 4 molecules ABCD

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