PDB-6ux3: Crystal structure of acetoin dehydrogenase from Enterobacter cloacae

ID or keywords:

Entry

Database: PDB / ID: 6ux3

Title

Crystal structure of acetoin dehydrogenase from Enterobacter cloacae

Components

Acetoin dehydrogenase

Keywords

OXIDOREDUCTASE / CSGID /

structural genomics / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

oxidoreductase activity
Similarity search - Function

Biological species

Enterobacter cloacae subsp. cloacae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.198 Å

Authors

Chang, C. / Skarina, T. / Mesa, N. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal structure of acetoin dehydrogenase from Enterobacter cloacae
Authors: Chang, C. / Skarina, T. / Mesa, N. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Nov 6, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 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	6ux3.cif.gz	376.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6ux3.ent.gz	309.2 KB	Display	PDB format
PDBx/mmJSON format	6ux3.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/ux/6ux3 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/6ux3	HTTPS FTP

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Related structure data

Related structure data	3sj7S S: Starting model for refinement
Similar structure data	5er6-d 3grk-2 1dfh-1 5oif-1 5cpb-1 5g0t-d 3vs8-1 5ugs-1 4oxy-d 5ugs-2 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: CSGID-IDP96727

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: Acetoin dehydrogenase

B: Acetoin dehydrogenase

C: Acetoin dehydrogenase

D: Acetoin dehydrogenase

hetero molecules

110 kDa, 4 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)	64.070, 99.836, 82.217
Angle α, β, γ (deg.)	90.000, 98.890, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Acetoin dehydrogenase / Mass: 27429.041 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria) Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_03449 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3CM71
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.59 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350, 0.1M calcium acetate, 5mM NAD

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97918 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 5, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 2.198→50 Å / Num. obs: 51666 / % possible obs: 99.5 % / Redundancy: 6.9 % / R_merge(I) obs: 0.064 / R_pim(I) all: 0.026 / R_rim(I) all: 0.069 / Χ²: 0.926 / Net I/σ(I): 11.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.2-2.24	6.5	1.078	2583	0.796	0.457	1.173	0.87	99.5
2.24-2.28	6.6	0.83	2562	0.832	0.347	0.901	1.016	99.5
2.28-2.32	6.8	0.764	2547	0.864	0.315	0.828	0.904	99.5
2.32-2.37	6.8	0.578	2578	0.9	0.238	0.626	0.909	99.4
2.37-2.42	6.4	0.459	2555	0.937	0.195	0.5	0.925	98.5
2.42-2.48	7	0.418	2579	0.949	0.17	0.452	0.924	99.7
2.48-2.54	7.2	0.335	2579	0.973	0.134	0.361	0.942	99.7
2.54-2.61	7.2	0.261	2556	0.977	0.104	0.281	0.953	99.6
2.61-2.69	7.1	0.199	2590	0.987	0.08	0.215	0.973	99.8
2.69-2.77	7	0.168	2604	0.986	0.068	0.182	0.962	99.6
2.77-2.87	6.9	0.128	2555	0.99	0.052	0.139	0.998	99.6
2.87-2.99	6.5	0.1	2554	0.993	0.042	0.108	0.99	98.8
2.99-3.12	7.2	0.089	2601	0.994	0.036	0.096	0.967	99.7
3.12-3.29	7.2	0.073	2594	0.993	0.03	0.079	0.949	99.8
3.29-3.49	7.1	0.067	2585	0.994	0.027	0.072	0.965	99.7
3.49-3.76	7	0.06	2598	0.995	0.024	0.065	0.962	99.7
3.76-4.14	6.9	0.057	2588	0.996	0.023	0.061	0.918	99.1
4.14-4.74	7.2	0.055	2594	0.996	0.022	0.06	0.87	99.8
4.74-5.97	6.8	0.054	2606	0.996	0.022	0.058	0.787	98.9
5.97-50	7	0.056	2658	0.995	0.023	0.061	0.74	99.4

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3sj7

3sj7

Resolution: 2.198→49.918 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.03

	R_factor	Num. reflection	% reflection
R_free	0.2361	2292	4.9 %
R_work	0.1763	-	-
obs	0.1792	46778	89.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 121.59 Å² / B_iso mean: 36.6782 Å² / B_iso min: 5.57 Å²

Refinement step

Cycle: final / Resolution: 2.198→49.918 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7345	0	13	378	7736
B_iso mean	-	-	62.28	37.82	-
Num. residues	-	-	-	-	988

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.1985-2.2463	0.2925	53	0.2537	1085	36
2.2463-2.2985	0.3169	62	0.2547	1514	48
2.2985-2.356	0.3006	117	0.2425	2182	70
2.356-2.4197	0.3343	161	0.251	2727	90
2.4197-2.4909	0.3522	137	0.2407	3068	99
2.4909-2.5713	0.2997	162	0.2237	3085	100
2.5713-2.6632	0.2736	171	0.2103	3075	100
2.6632-2.7698	0.2649	160	0.2095	3049	100
2.7698-2.8959	0.2779	162	0.2034	3059	100
2.8959-3.0485	0.272	162	0.2037	3076	99
3.0485-3.2395	0.2378	142	0.1955	3071	100
3.2395-3.4896	0.2658	154	0.1809	3094	100
3.4896-3.8406	0.2108	173	0.1551	3077	99
3.8406-4.3961	0.1723	167	0.1341	3070	99
4.3961-5.5374	0.1788	153	0.1252	3119	100
5.5374-49.918	0.1867	156	0.1426	3135	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	0.015	0.0049	0.0093	0.0026	-0.0006	0.0308	0.0186	0.0078	-0.0044	-0.027	0.0109	0.0083	0.0153	-0.0168	0.0391	0.2914	-0.1359	-0.0878	0.1931	0.0784	0.1235	32.1478	40.4052	31.871
2	0.0003	-0.0003	-0.001	-0.0001	0.0018	0.0038	0.059	0.0553	0.0024	-0.0233	0.0114	0.0104	0.0331	-0.0001	0	0.4832	-0.0553	-0.1308	0.2726	0.0814	0.2046	30.5098	37.4917	24.8189
3	0.0014	-0.0007	-0.0014	0.0014	0.0013	0.0057	-0.0016	0.0407	0.0262	-0.0249	0.0274	0.0222	0.024	0.0058	0	0.6345	0.0744	-0.0194	0.4241	-0.031	0.2891	41.581	32.5303	25.9316
4	-0.0004	0.0005	-0.0004	0.0003	0.0002	0.0008	0.0391	0.0259	0.0292	-0.007	-0.0196	-0.0066	0.0003	0.0133	0.0183	0.3186	-0.0885	0.0644	0.2218	0.0999	0.0405	43.3493	40.744	28.5985
5	0.1518	0.0069	0.0342	0.0001	0.001	0.0081	0.1029	0.1013	-0.0263	-0.0389	0.0284	-0.0339	0.0503	0.1022	0.0942	0.3197	-0.0289	0.0236	0.1162	-0.0385	0.0685	43.6908	24.1717	38.802
6	0.0555	0.0119	0.0148	0.007	0.0061	0.0065	0.0739	0.0274	0.0176	-0.0537	0.0265	0.0272	0.0894	0.055	0.0971	0.2459	-0.1237	-0.0152	0.0694	0.0158	0.144	40.8801	32.7344	45.9837
7	0.0107	0.0045	0.0012	0.0022	0.0015	0.0007	0.0128	0.0086	-0.0154	-0.0019	-0.0093	0.0135	0.0045	-0.0114	0.0082	0.2296	-0.2239	-0.1366	0.2028	-0	0.2743	18.1251	27.1525	44.3504
8	0.0121	0.005	-0.0007	0.0066	-0.0069	0.0077	0.016	0	0.0362	-0.0264	0.0129	-0.014	-0.0131	-0.0186	0.0108	0.1885	-0.1518	-0.0646	0.1617	0.0349	0.1845	32.7635	43.246	44.5688
9	0.004	0.0058	-0.0024	0.0106	-0.003	0.0089	-0.0098	-0.0006	-0.0029	-0.0147	0.0183	-0.0015	-0.0063	0.0011	0.0017	0.2121	-0.19	-0.0759	0.1396	0.0602	0.2899	24.9205	27.4881	56.4571
10	0.0083	-0.0037	-0.001	0.0092	-0.023	0.0735	0.0122	-0.0233	0.071	-0.0203	0.0703	-0.017	-0.0481	-0.0123	0.037	0.1858	-0.0523	-0.0291	0.1458	-0.0517	0.3351	20.6455	59.6759	56.5864
11	0.0813	0.0834	-0.0252	0.1466	-0.1053	0.125	0.0056	-0.0461	0.1122	0.1391	0.1121	0.0648	-0.0476	0.0057	0.114	0.2054	0.0881	-0.0187	0.2028	-0.1044	0.1718	23.1195	51.6225	70.4126
12	0.0321	-0.084	-0.0339	0.2032	-0.0184	0.2187	-0.0026	-0.0146	0.1002	-0.0502	0.1716	0.037	-0.1383	-0.0211	0.4504	-0.3562	-0.4377	-0.0317	-0.1926	-0.0114	0.101	30.7157	44.7295	59.0979
13	0.0005	-0.0003	0	0.003	0.0029	0.003	-0.0091	-0.0114	-0.0119	0.0129	0.0105	0.0068	0.0169	0.0096	0.0033	0.196	0.0168	0.0581	0.3466	0.1851	0.1548	39.954	18.8999	87.6775
14	0.0102	-0.0024	0.0095	0.0004	-0.0021	0.0145	0.0227	-0.0362	-0.0276	0.044	-0.0324	0.0117	0.0365	-0.0259	-0.0135	0.3242	0.1231	0.052	0.5676	0.1693	0.2002	36.2258	21.1736	94.3319
15	0.0235	0.0177	-0.0296	0.0751	-0.0158	0.0452	0.0219	-0.0321	0.0406	0.0921	0.075	0.103	-0.0353	0.0267	0.081	0.1772	0.0332	0.07	0.3946	0.1299	0.0605	32.4368	31.1515	86.1509
16	0.0125	0.0058	0.0076	0.0391	0.0095	0.0122	0.0082	-0.0193	0.0201	0.0712	0.0732	0.0018	-0.0103	0.0341	0.0555	0.2019	0.0842	0.0389	0.4743	0.0056	0.0819	33.8131	37.3522	83.8812
17	0.0275	-0.0042	-0.0097	0.0246	-0.0026	0.0216	-0.0021	-0.0237	0.0041	-0.0057	0.04	0.0584	0.0083	0.0166	0.0263	0.0788	-0.0811	0.0167	0.2278	0.0717	0.0996	34.8716	28.2505	74.0644
18	0.0503	-0.0074	-0.0052	0.0404	0.0007	0.0385	0.0007	-0.0747	0.0022	0.038	0.0733	0.0199	-0.0132	-0.0108	0.0927	0.0904	-0.054	0.0253	0.2004	0.0351	0.0667	37.0211	28.7921	75.8481
19	0.0045	-0.0024	-0.0023	0.003	-0.003	0.0351	-0.0172	-0.0606	-0.0597	-0.0066	0.0388	0.0417	0.0679	0.0318	0.0089	0.1141	-0.0449	0.0157	0.1966	0.1376	0.1807	38.8475	16.7397	73.0372
20	0.001	0.0004	-0.0035	0.0045	0.0017	0.0097	-0.0159	-0.0088	-0.0201	-0.0091	-0.0184	0.0223	0.0031	0.0031	-0.0144	0.1755	-0.1158	-0.0377	0.1007	0.0583	0.2444	30.7218	18.96	61.2149
21	0.0208	0.0012	0.0022	0.0226	0.0052	0.0274	0.033	-0.0346	-0.1327	0.039	0.0348	-0.0409	0.0923	0.0521	0.0415	0.4384	0.2142	0.0071	0.2757	0.1154	0.3018	58.6216	5.0546	60.1595
22	0.1163	-0.042	0.0283	0.0994	-0.0383	0.2292	0.0929	-0.0367	-0.1019	-0.0995	-0.0077	-0.1174	0.1863	0.2435	0.1717	0.0926	-0.0156	0.0311	0.0664	0.0382	0.1102	49.7403	20.9772	58.6035

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 1 through 24 )	A	1 - 24
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 50 )	A	25 - 50
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 51 through 69 )	A	51 - 69
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 70 through 86 )	A	70 - 86
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 87 through 129 )	A	87 - 129
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 130 through 183 )	A	130 - 183
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 184 through 213 )	A	184 - 213
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 214 through 235 )	A	214 - 235
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 236 through 252 )	A	236 - 252
10	X-RAY DIFFRACTION	10	chain 'B' and (resid -1 through 50 )	B	-1 - 50
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 51 through 112 )	B	51 - 112
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 113 through 252 )	B	113 - 252
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 2 through 24 )	C	2 - 24
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 25 through 65 )	C	25 - 65
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 66 through 100 )	C	66 - 100
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 101 through 129 )	C	101 - 129
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 130 through 150 )	C	130 - 150
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 151 through 199 )	C	151 - 199
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 200 through 235 )	C	200 - 235
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 236 through 252 )	C	236 - 252
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 1 through 86 )	D	1 - 86
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 87 through 252 )	D	87 - 252

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Yorodumi