PDB-8uzo: Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from K...

ID or keywords:

Entry

Database: PDB / ID: 8uzo

Title

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (ADP bound)

Components

Betaine aldehyde dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Betaine aldehyde dehydrogenase (BetB)

Function / homology

Function and homology information

betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / glycine betaine biosynthetic process from choline / metal ion binding
Similarity search - Function

Biological species

Klebsiella aerogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (ADP bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A.

History

Deposition	Nov 15, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 6, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8uzo.cif.gz	757.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8uzo.ent.gz	627.5 KB	Display	PDB format
PDBx/mmJSON format	8uzo.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/uz/8uzo ftp://data.pdbj.org/pub/pdb/validation_reports/uz/8uzo	HTTPS FTP

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Related structure data

Similar structure data	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	#127 - Jul 2010 Crystallins similarity (7) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (7)

Deposited unit

A: Betaine aldehyde dehydrogenase

B: Betaine aldehyde dehydrogenase

C: Betaine aldehyde dehydrogenase

D: Betaine aldehyde dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	83.801, 100.578, 123.753
Angle α, β, γ (deg.)	90.00, 95.90, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Betaine aldehyde dehydrogenase Mass: 54062.281 Da / Num. of mol.: 4 / Mutation: V62A, Q485P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Strain: KCTC 2190 / Gene: betB_3 / Plasmid: KlaeA.00020.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A447LC14
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.73 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: JCSG+ G8: 20% PEG 3350, 0.15 M DL-malic acid, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. Overnight soak in 20mM ADP in crystallant. Plate: 13677, well G8 drop 1. Puck: PSL-0505, Cryo: 30% PEG3350 + 70% crystallant

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 9, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.1→123.1 Å / Num. obs: 118414 / % possible obs: 99.5 % / Redundancy: 3.7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.072 / R_pim(I) all: 0.043 / R_rim(I) all: 0.084 / Χ²: 0.98 / Net I/σ(I): 10.3 / Num. measured all: 440006
Reflection shell	Resolution: 2.1→2.15 Å / % possible obs: 99.5 % / Redundancy: 3.9 % / R_merge(I) obs: 0.748 / Num. measured all: 33842 / Num. unique obs: 8728 / CC_1/2: 0.778 / R_pim(I) all: 0.436 / R_rim(I) all: 0.867 / Χ²: 0.98 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→83.36 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2127	5848	4.94 %
R_work	0.1867	-	-
obs	0.188	118275	99.27 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.1→83.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14757	0	112	519	15388

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	15375
X-RAY DIFFRACTION	f_angle_d	0.753	20930
X-RAY DIFFRACTION	f_dihedral_angle_d	12.89	5692
X-RAY DIFFRACTION	f_chiral_restr	0.048	2370
X-RAY DIFFRACTION	f_plane_restr	0.011	2731

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 (%)
2.1-2.12	0.3196	193	0.2822	3735	X-RAY DIFFRACTION	99
2.12-2.15	0.3181	176	0.2706	3772	X-RAY DIFFRACTION	99
2.15-2.18	0.3286	225	0.2646	3655	X-RAY DIFFRACTION	99
2.18-2.2	0.3271	194	0.2616	3755	X-RAY DIFFRACTION	99
2.2-2.23	0.2935	202	0.2548	3693	X-RAY DIFFRACTION	99
2.23-2.26	0.2851	196	0.2527	3755	X-RAY DIFFRACTION	100
2.26-2.29	0.3093	199	0.2509	3773	X-RAY DIFFRACTION	100
2.29-2.33	0.264	207	0.2389	3710	X-RAY DIFFRACTION	99
2.33-2.37	0.2962	196	0.2361	3706	X-RAY DIFFRACTION	99
2.37-2.4	0.3064	204	0.2375	3740	X-RAY DIFFRACTION	99
2.4-2.45	0.2634	185	0.2279	3777	X-RAY DIFFRACTION	100
2.45-2.49	0.2834	180	0.2162	3759	X-RAY DIFFRACTION	100
2.49-2.54	0.2683	175	0.2137	3787	X-RAY DIFFRACTION	100
2.54-2.59	0.253	205	0.2053	3715	X-RAY DIFFRACTION	99
2.59-2.65	0.2578	194	0.2069	3740	X-RAY DIFFRACTION	99
2.65-2.71	0.2538	198	0.2108	3750	X-RAY DIFFRACTION	100
2.71-2.78	0.2604	175	0.2148	3768	X-RAY DIFFRACTION	100
2.78-2.85	0.2457	196	0.2218	3745	X-RAY DIFFRACTION	99
2.85-2.93	0.2755	192	0.2298	3740	X-RAY DIFFRACTION	100
2.93-3.03	0.2926	186	0.2295	3771	X-RAY DIFFRACTION	99
3.03-3.14	0.2446	205	0.2174	3735	X-RAY DIFFRACTION	99
3.14-3.26	0.2397	190	0.2151	3775	X-RAY DIFFRACTION	99
3.26-3.41	0.2273	202	0.2043	3678	X-RAY DIFFRACTION	99
3.41-3.59	0.2228	195	0.196	3747	X-RAY DIFFRACTION	99
3.59-3.82	0.2013	181	0.1763	3765	X-RAY DIFFRACTION	98
3.82-4.11	0.1763	172	0.1512	3722	X-RAY DIFFRACTION	98
4.11-4.52	0.1228	213	0.1255	3737	X-RAY DIFFRACTION	99
4.52-5.18	0.1335	200	0.1221	3781	X-RAY DIFFRACTION	99
5.18-6.52	0.1843	212	0.1564	3807	X-RAY DIFFRACTION	99
6.52-83.36	0.1546	200	0.1482	3834	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	0.0459	-0.0723	-0.0334	0.1151	0.0511	0.0404	-0.0321	-0.0218	-0.2896	-0.1327	-0.0877	-0.3172	0.1264	0.3532	-0.0001	0.3438	0.0067	0.0645	0.404	0.0345	0.4277	93.4256	-14.0216	19.4222
2	0.0722	0.0098	-0.1211	0.1434	-0.0021	0.2838	-0.0519	-0.0288	-0.1188	-0.1221	-0.0996	-0.1269	0.0303	0.1344	-0.0002	0.3133	-0.0104	-0.0214	0.3276	0.0095	0.3544	83.0384	-11.5504	22.5991
3	0.0933	0.0345	-0.0589	0.0635	-0.0627	0.0676	0.1701	0.0204	0.0516	-0.0584	-0.0614	0.1529	-0.1009	0.0522	0.0094	0.4102	-0.0633	-0.0371	0.3736	-0.035	0.359	76.6231	7.3754	25.7206
4	0.1061	0.0874	-0.0473	0.1993	0.0284	0.1669	0.1241	-0.0971	0.2027	-0.0149	-0.0205	-0.0235	-0.3282	0.155	0.0585	0.4546	-0.0962	0.0338	0.2877	0.0098	0.382	78.7797	17.7714	30.8669
5	0.1264	-0.011	-0.1299	0.0011	0.0091	0.1308	-0.0303	0.1229	-0.0955	-0.0616	-0.0555	0.0015	-0.0516	-0.1118	-0	0.3299	-0.0185	-0.026	0.3096	-0.0266	0.3273	65.9398	-12.21	20.6629
6	0.0651	0.0754	0.0711	0.0957	0.0896	0.0793	-0.0254	0.2229	-0.1	-0.0681	0.0694	0.3392	-0.0178	-0.2321	-0.0003	0.2961	-0.0706	0.0341	0.4503	-0.0331	0.4991	26.522	-24.6779	37.3669
7	0.0663	0.0539	-0.0731	0.2103	-0.0339	0.0805	-0.083	0.1264	-0.1239	0.0241	-0.0063	0.089	0.0499	-0.2296	-0.0001	0.3073	-0.0328	-0.0063	0.365	-0.0261	0.3912	36.9893	-20.8467	37.8606
8	0.0562	0.027	-0.018	0.0183	0.0121	0.0762	0.0045	-0.1858	-0.0326	0.0335	0.04	0.0248	-0.015	0.0236	0	0.3413	0.0291	0.0283	0.3428	-0.0067	0.3806	43.6282	-9.7907	53.6647
9	0.0696	-0.0586	-0.0525	0.0514	0.0548	0.0689	0.0202	-0.3163	0.1176	0.2205	-0.0329	0.1919	-0.1086	-0.2206	0	0.3885	0.0556	0.0593	0.4713	-0.009	0.3749	33.4351	1.1914	61.7244
10	0.2048	0.0552	-0.087	0.1408	0.0829	0.1142	-0.0632	-0.1538	-0.0718	0.0683	0.0385	-0.0022	0.0183	-0.0657	0.0017	0.3557	0.0026	-0.007	0.3845	0.0177	0.3222	50.7746	-10.6501	51.1597
11	0.0891	-0.0933	-0.0419	0.1019	0.0411	0.0222	-0.0006	0.274	0.0848	-0.1199	-0.0325	0.0332	-0.1302	-0.1083	-0.0996	0.4805	0.1978	-0.0005	0.7693	0.1824	0.2991	45.6245	4.1162	-6.5583
12	0.0273	-0.017	-0.0098	0.0385	0.0374	0.0358	0.0979	0.1554	0.2021	0.0352	-0.0773	-0.003	-0.1373	-0.3367	0	0.3331	0.0603	-0.002	0.4552	0.0561	0.3585	46.3501	2.074	15.4746
13	0.3176	-0.0341	-0.2134	0.1622	0.1202	0.2116	0.0923	0.3095	0.0125	0.0132	-0.0588	-0.042	-0.0176	-0.2208	0.1806	0.2581	0.04	-0.0411	0.4836	0.0204	0.2173	51.4173	-4.8236	10.1316
14	0.3324	-0.1692	0.1916	0.0869	-0.0984	0.1158	-0.0744	0.3199	-0.056	-0.0565	-0.1186	0.0637	0.0608	-0.2048	-0.1321	0.4067	-0.0614	0.0098	0.6119	-0.2032	0.393	61.3234	-19.9051	0.5284
15	0.0251	0.0191	-0.0099	0.0168	-0.0064	0.0058	-0.0589	0.1546	-0.1159	-0.1443	0.0326	-0.0046	0.049	-0.2485	-0.0343	0.5126	-0.0988	0.0135	0.8526	-0.3536	0.4313	52.1461	-31.0566	-9.4834
16	0.0062	0.0131	0.0079	0.0376	-0.0069	0.0746	-0.037	0.1341	-0.0834	-0.0308	-0.006	0.0226	-0.0438	-0.0814	-0.103	0.5501	-0.0597	0.02	0.9077	-0.2619	0.3247	58.7213	-21.405	-19.1198
17	0.184	0.2218	0.0588	0.4027	0.017	0.0464	-0.0262	0.3938	-0.2754	-0.0527	-0.0396	-0.1311	0.1159	-0.1668	-0.1257	0.4389	-0.0561	0.0681	0.5527	-0.2524	0.4384	65.4299	-28.9538	-2.1271
18	0.1316	0.0657	-0.0947	0.0313	-0.046	0.0675	-0.0978	0.1339	-0.0557	-0.0922	0.012	0.0326	-0.1728	-0.026	0	0.2756	-0.0347	-0.0332	0.315	-0.0284	0.255	63.8134	-9.8149	21
19	0.0001	0.0034	-0.0004	0.0283	-0.0304	0.0512	0.0163	-0.0836	-0.0811	-0.0582	-0.0084	-0.007	0.2477	-0.0304	0.0258	0.5723	-0.0177	-0.0388	0.7126	0.3726	0.4742	74.3794	-40.7773	64.0741
20	0.0209	0.0038	-0.0154	0.3133	0.0548	0.0781	-0.0319	-0.4561	-0.1752	0.0482	-0.0722	-0.1725	-0.046	-0.0991	0.0108	0.3433	0.0462	-0.0266	0.6056	0.1179	0.3533	73.945	-22.0218	53.0833
21	0.124	0.0493	0.1408	0.2385	-0.0609	0.3242	0.0208	-0.2579	-0.1218	-0.0409	-0.0387	-0.0239	0.1022	-0.0162	-0.3303	0.3338	0.0528	0.0104	0.2509	0.1901	0.3749	69.4226	-28.3383	43.8747
22	0.0557	0.02	0.0498	0.033	0.0102	0.047	0.0796	-0.3522	-0.1827	0.106	-0.0977	0.025	0.1259	-0.1026	-0.0339	0.3807	-0.036	-0.0301	0.7255	0.2729	0.4703	67.9637	-31.6853	56.7211
23	0.8254	-0.0652	0.5631	0.0105	-0.0303	0.4224	0.0346	-0.2427	-0.2928	-0.0731	0.1232	0.0247	0.3093	-0.2456	0.2058	0.7059	-0.1196	0.0223	0.2718	0.1256	0.788	59.0324	-44.8499	39.465
24	0.0584	-0.0553	-0.0308	0.0522	0.0301	0.0164	-0.1431	-0.0276	-0.1941	0.0301	-0.0229	0.0627	0.1893	0.0268	-0.2957	1.1609	-0.0547	0.0072	0.3323	0.1897	1.1127	68.5398	-58.5822	33.4616
25	0.0047	0.0174	0.0093	0.0619	0.0321	0.0166	0.0436	-0.0235	-0.0173	0.0307	-0.0122	-0.0071	0.0413	-0.0169	0.1166	1.3237	-0.1829	0.072	0.5242	0.3629	1.1865	61.9904	-63.2875	46.2426
26	0.0318	-0.0442	0.0063	0.0625	-0.0061	0.0296	-0.0664	0.0057	-0.1452	0.1277	-0.0035	0.0059	0.1092	-0.0359	-0.1213	0.9844	-0.3591	-0.0032	0.4504	0.1794	1.0588	55.2194	-56.6557	36.1859
27	0.1692	-0.1761	0.2375	0.5389	-0.1381	0.4195	-0.0617	-0.0928	-0.1948	0.1369	0.0527	0.0988	0.1519	-0.2203	-0.0235	0.3121	-0.1121	0.0381	0.2114	0.0497	0.4656	55.8047	-29.7332	34.6753

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 81 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 82 through 230 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 231 through 290 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 291 through 441 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 442 through 490 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 3 through 81 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 82 through 230 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 231 through 290 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 291 through 363 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 364 through 490 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 3 through 42 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 43 through 81 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 82 through 230 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 231 through 290 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 291 through 330 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 331 through 363 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 364 through 441 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 442 through 490 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 5 through 42 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 43 through 81 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 82 through 168 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 169 through 230 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 231 through 290 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 291 through 330 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 331 through 363 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 364 through 409 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 410 through 490 )

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Yorodumi