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

ID or keywords:

Entry

Database: PDB / ID: 8uzk

Title

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (NADP+ 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: 1.9 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 (NADP+ 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	8uzk.cif.gz	753.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8uzk.ent.gz	624.2 KB	Display	PDB format
PDBx/mmJSON format	8uzk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8uzk_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	8uzk_full_validation.pdf.gz	2.1 MB	Display
Data in XML	8uzk_validation.xml.gz	74 KB	Display
Data in CIF	8uzk_validation.cif.gz	106.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uz/8uzk ftp://data.pdbj.org/pub/pdb/validation_reports/uz/8uzk	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

220 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)	81.651, 99.365, 124.513
Angle α, β, γ (deg.)	90.00, 96.61, 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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#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.: 976 / 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: 2.32 Å³/Da / Density % sol: 46.99 %
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. Plate: 13677, well G8 drop 1. Overnight soak with 10mM NADP+ in crystallant. Puck: PSL-0415, Cryo: 30% ...Details: JCSG+ G8: 20% PEG 3350, 0.15 M DL-malic acid, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. Plate: 13677, well G8 drop 1. Overnight soak with 10mM NADP+ in crystallant. Puck: PSL-0415, Cryo: 30% PEG3350 + 70% crystallant

Crystal

Density Matthews: 2.32 Å³/Da / Density % sol: 46.99 %

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. Plate: 13677, well G8 drop 1. Overnight soak with 10mM NADP+ in crystallant. Puck: PSL-0415, Cryo: 30% ...

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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: 1.9→123.69 Å / Num. obs: 154537 / % possible obs: 99.5 % / Redundancy: 4.4 % / CC_1/2: 0.994 / R_merge(I) obs: 0.127 / R_pim(I) all: 0.068 / R_rim(I) all: 0.145 / Χ²: 0.96 / Net I/σ(I): 7.8 / Num. measured all: 677985
Reflection shell	Resolution: 1.9→1.95 Å / % possible obs: 99.8 % / Redundancy: 4.2 % / R_merge(I) obs: 0.9 / Num. measured all: 47739 / Num. unique obs: 11450 / CC_1/2: 0.607 / R_pim(I) all: 0.486 / R_rim(I) all: 1.027 / Χ²: 0.96 / Net I/σ(I) obs: 1.8

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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: 1.9→81.11 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1989	7758	5.03 %
R_work	0.1608	-	-
obs	0.1627	154285	99.29 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→81.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14769	0	244	976	15989

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	15596
X-RAY DIFFRACTION	f_angle_d	0.869	21262
X-RAY DIFFRACTION	f_dihedral_angle_d	13.689	5757
X-RAY DIFFRACTION	f_chiral_restr	0.053	2393
X-RAY DIFFRACTION	f_plane_restr	0.008	2762

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 (%)
1.9-1.92	0.3115	270	0.2449	4868	X-RAY DIFFRACTION	100
1.92-1.94	0.2664	285	0.2339	4899	X-RAY DIFFRACTION	100
1.94-1.97	0.2957	247	0.2262	4810	X-RAY DIFFRACTION	100
1.97-1.99	0.2824	252	0.2245	4886	X-RAY DIFFRACTION	99
1.99-2.02	0.2561	216	0.2093	4813	X-RAY DIFFRACTION	98
2.02-2.05	0.2535	263	0.2051	4833	X-RAY DIFFRACTION	98
2.05-2.08	0.244	249	0.1877	4897	X-RAY DIFFRACTION	99
2.08-2.11	0.242	262	0.1831	4884	X-RAY DIFFRACTION	100
2.11-2.14	0.2523	249	0.1768	4846	X-RAY DIFFRACTION	100
2.14-2.17	0.2112	264	0.1753	4916	X-RAY DIFFRACTION	100
2.17-2.21	0.2137	262	0.1641	4936	X-RAY DIFFRACTION	100
2.21-2.25	0.2275	263	0.1671	4836	X-RAY DIFFRACTION	100
2.25-2.3	0.227	257	0.1665	4925	X-RAY DIFFRACTION	100
2.3-2.34	0.2167	271	0.1599	4880	X-RAY DIFFRACTION	100
2.34-2.39	0.1922	267	0.1546	4883	X-RAY DIFFRACTION	100
2.39-2.45	0.2058	230	0.1513	4918	X-RAY DIFFRACTION	100
2.45-2.51	0.2012	263	0.1514	4887	X-RAY DIFFRACTION	100
2.51-2.58	0.1923	272	0.1558	4900	X-RAY DIFFRACTION	100
2.58-2.65	0.2029	257	0.1644	4909	X-RAY DIFFRACTION	99
2.65-2.74	0.2308	225	0.1685	4894	X-RAY DIFFRACTION	99
2.74-2.84	0.2029	255	0.1665	4887	X-RAY DIFFRACTION	99
2.84-2.95	0.2249	263	0.1689	4867	X-RAY DIFFRACTION	99
2.95-3.09	0.2004	264	0.1741	4904	X-RAY DIFFRACTION	99
3.09-3.25	0.2236	260	0.1809	4895	X-RAY DIFFRACTION	99
3.25-3.45	0.2052	269	0.1704	4866	X-RAY DIFFRACTION	99
3.45-3.72	0.1759	277	0.1493	4847	X-RAY DIFFRACTION	98
3.72-4.09	0.1623	241	0.1357	4867	X-RAY DIFFRACTION	98
4.09-4.69	0.1314	258	0.1125	4910	X-RAY DIFFRACTION	99
4.69-5.9	0.1567	275	0.1301	4913	X-RAY DIFFRACTION	99
5.9-81.11	0.1766	272	0.1578	4951	X-RAY DIFFRACTION	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	0.0232	0.0202	-0.0217	0.9379	0.155	0.2402	-0.0902	0.1538	-0.121	-0.1541	0.1884	-0.593	-0.0281	0.348	-0.1145	0.1475	-0.0292	0.046	0.3315	-0.0091	0.2526	98.9634	-4.179	17.2688
2	0.4066	-0.1294	-0.0256	0.6666	0.3499	0.2545	-0.0083	0.0435	-0.1979	-0.0404	-0.0311	-0.1429	0.0674	0.0984	0.0003	0.1802	0.0035	-0.0003	0.2046	-0.0216	0.1906	84.3041	-19.9193	21.8698
3	0.0859	0.2709	0.0767	0.3154	0.0675	0.0914	0.0248	0.0226	-0.0564	0.0222	-0.0156	-0.0741	-0.0229	-0.008	0	0.1431	0.0014	0.0016	0.1551	0.0043	0.164	77.3325	-11.0835	26.7569
4	0.7439	-0.0545	-0.0016	0.5989	0.4072	0.2601	0.0398	0.1359	-0.0163	-0.1794	-0.0592	-0.1131	-0.0556	0.1421	0	0.1933	0.0244	0.0136	0.22	0.0055	0.1752	84.4913	-7.5504	15.3147
5	0.1709	0.2026	0.015	0.7166	0.0245	0.1719	0.0481	0.0271	-0.041	0.0212	0.0057	0.0628	-0.0981	0.018	0	0.1819	-0.0025	0.0072	0.1714	-0.0049	0.1733	73.0094	14.88	34.2469
6	0.5352	0.2191	0.1237	0.4738	0.0137	0.0267	0.0259	0.055	0.1499	0.1312	-0.0063	-0.1609	-0.091	0.102	0.0002	0.217	-0.006	-0.0001	0.1761	0.0227	0.1832	88.3497	19.1852	29.0135
7	0.35	0.198	0.0412	0.5063	-0.089	0.1988	0.0546	0.0312	0.0655	-0.0148	-0.021	0.07	-0.0344	0.0069	0	0.1916	-0.0008	0.0006	0.1576	0.0103	0.2	72.4149	20.9601	27.799
8	0.0646	0.1554	0.0182	0.2863	0.2553	0.2136	0.0046	0.0339	0.0077	-0.0075	0.0227	0.0538	-0.0228	0.0346	0	0.1823	0.0049	-0	0.1682	0.0055	0.1815	63.0343	-3.5356	25.4056
9	0.7478	-0.3632	-0.2618	0.8908	0.2525	0.668	-0.0024	0.1004	-0.1914	-0.0032	-0.0115	0.1684	0.1543	-0.1623	0.0105	0.1222	-0.0211	-0.0036	0.1878	0.0002	0.2452	25.0214	-26.5005	36.4212
10	0.0498	0.0109	-0.109	0.059	0.0194	0.2468	0.0403	0.0625	-0.0033	-0.0076	-0.0357	0.0196	-0.0335	-0.08	-0	0.1776	0.0247	0.0099	0.2053	0.0101	0.1952	38.5002	-18.2807	34.9272
11	0.8147	0.3114	-0.1397	0.538	0.3759	0.3576	0.0381	-0.0313	-0.1973	0.0919	0.0036	0.0899	0.0566	0.0029	0	0.1908	-0.0005	-0.0004	0.2028	0.0418	0.2305	31.8892	-27.8558	42.7001
12	0.6477	0.1401	-0.1902	0.0504	0.0372	0.1033	0.0991	-0.1545	-0.0583	0.0803	0.0149	-0.0015	-0.054	-0.0262	0.0609	0.2151	-0.0016	0.0196	0.1963	0.0039	0.2246	43.8833	-6.4091	52.3567
13	0.6957	0.0113	-0.0172	0.1245	-0.0509	0.1829	0.0236	-0.1506	0.0016	0.1156	0.0416	0.0843	-0.0814	-0.0293	0.1142	0.2946	-0.0067	0.0703	0.2436	-0.0303	0.2012	38.2156	3.6183	58.68
14	0.3619	0.065	0.0963	1.0063	0.2262	0.2666	0.0364	-0.1177	0.0594	0.0633	-0.0149	0.2809	-0.0594	-0.176	0.0645	0.2534	0.0258	0.0924	0.3318	-0.0104	0.2227	25.3426	-4.6903	61.0754
15	0.3018	0.0618	-0.3289	0.1816	0.1033	0.3341	0.1011	-0.2723	-0.0233	0.1429	-0.0491	0.0132	-0.0483	0.0104	0	0.2821	-0.0042	0.0402	0.2745	-0.0108	0.1981	40.6628	-4.0611	64.0812
16	0.0767	-0.1779	-0.0703	0.4919	-0.0467	0.0247	0.0246	-0.0077	-0.0196	0.0751	-0.0143	0.0306	-0.0077	-0.0235	0	0.1904	-0.0107	0.008	0.1949	-0.0001	0.1752	52.5971	-15.4857	43.0669
17	0.2801	-0.0986	0.0211	0.3288	0.2861	0.2537	-0.0198	0.1562	0.2124	-0.2471	-0.0939	0.3663	-0.4038	-0.3184	-0.0663	0.2795	0.0384	-0.0392	0.2436	0.0827	0.283	43.7227	4.3545	-6.8125
18	0.1761	-0.0698	0.0964	0.5119	0.504	0.5095	0.0122	-0.0683	0.1977	0.0561	0.0145	0.0842	-0.1642	-0.1986	-0.0061	0.1974	0.0322	-0.0046	0.1956	-0.0104	0.232	43.9573	1.9159	15.2839
19	0.2338	0.1417	0.1329	-0.1571	0.1458	0.0501	0.0334	0.0334	-0.0106	0.0489	0.0058	0.0002	-0.0386	-0.0369	0.0004	0.1729	0.0129	-0.016	0.175	0.007	0.1562	48.9213	-8.9095	13.2244
20	0.1924	-0.2458	0.2279	0.903	0.2827	0.6184	0.0137	0.1426	0.1172	-0.0648	0.0912	-0.0324	-0.1313	0.056	-0	0.1983	0.0203	0.0065	0.2195	0.0118	0.1979	53.0268	1.2007	4.5081
21	0.5478	-0.1482	0.1955	0.0915	-0.2597	0.7765	-0.018	-0.0499	0.0437	0.1383	0.0316	0.005	0.0656	0.0295	-0.0003	0.1659	0.0183	-0.007	0.2049	-0.0287	0.1746	59.8269	-24.6531	1.965
22	0.1221	-0.1082	0.1296	0.1338	-0.1566	0.5204	0.0029	0.0209	0.0197	0.0612	0.0324	0.0584	0.0522	-0.0687	0	0.2005	0.0062	-0.0025	0.2408	-0.0135	0.2024	56.7784	-32.0054	-7.3613
23	0.4269	-0.2824	-0.4566	0.6568	0.151	0.3484	0.0002	0.164	0.0386	-0.1461	0.0049	-0.0502	-0.071	-0.0077	0	0.1843	0.0074	-0.0069	0.2115	-0.0112	0.1575	58.485	-23.4999	-12.9556
24	0.0231	0.1521	0.1281	0.3034	0.3279	0.5037	0.005	0.0049	-0.0081	-0.0078	-0.0023	-0.041	-0.0138	-0.017	0	0.1701	0.0101	-0.0065	0.178	0.0044	0.1812	62.8124	-17.3471	15.8638
25	0.1472	-0.066	0.2271	0.2059	0.0438	0.4466	0.0245	-0.0939	0.0254	0.2977	0.0206	-0.2639	0.0602	0.086	0.0008	0.2766	0.0035	-0.0503	0.23	0.0197	0.1976	72.7517	-40.0483	64.1766
26	0.5276	-0.0395	0.1081	0.5605	0.3982	0.2538	0.0056	-0.0819	0.018	0.0767	-0.0713	-0.0442	-0.1262	0.0372	-0	0.2001	0.0102	-0.0331	0.1555	-0.0041	0.1688	71.718	-21.3192	53.1248
27	0.1875	-0.1526	-0.1053	0.142	0.1065	-0.0446	0.03	-0.0144	-0.0079	-0.0273	-0.0177	-0.0155	0.0256	-0.0019	-0	0.1918	0.0135	-0.0129	0.1477	0.012	0.1709	67.7187	-27.8552	43.7579
28	0.1903	0.269	0.1511	0.5458	0.1923	0.9652	0.0409	-0.1052	-0.0188	0.0584	-0.0602	0.021	0.0337	-0.0747	0.0009	0.1899	0.0146	-0.017	0.1752	0.0037	0.1756	61.9331	-36.3247	49.1905
29	0.6821	-0.5843	0.2088	0.7366	-0.1179	0.4483	-0.0516	-0.0413	-0.1352	0.0312	0.051	0.0914	0.1194	-0.0477	-0.0002	0.249	-0.0143	0.0004	0.1651	0.0245	0.2094	61.5268	-57.8759	37.8109
30	0.0493	-0.1449	-0.0167	0.5431	-0.122	-0.149	0.0012	0	-0.0109	0.0843	0.0379	-0.0171	0.0237	-0.0101	0.0227	0.2058	-0.001	0.0057	0.1836	0.0093	0.167	54.3563	-29.9024	34.2822

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 81 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 82 through 168 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 169 through 244 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 245 through 312 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 313 through 363 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 364 through 409 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 410 through 490 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 3 through 81 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 82 through 168 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 169 through 244 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 245 through 276 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 277 through 312 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 313 through 363 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 364 through 409 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 410 through 490 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 3 through 42 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 43 through 81 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 82 through 168 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 169 through 244 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 245 through 276 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 277 through 312 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 313 through 409 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 410 through 490 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 5 through 42 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 43 through 81 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 82 through 168 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 169 through 276 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 277 through 409 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 410 through 490 )

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