PDB-8vr0: Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from K...

ID or keywords:

Entry

Database: PDB / ID: 8vr0

Title

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (GMP 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 KCTC 2190 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 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 (GMP bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A.

History

Deposition	Jan 19, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 31, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vr0.cif.gz	756.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8vr0.ent.gz	625.3 KB	Display	PDB format
PDBx/mmJSON format	8vr0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vr0_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8vr0_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8vr0_validation.xml.gz	71.4 KB	Display
Data in CIF	8vr0_validation.cif.gz	100.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vr/8vr0 ftp://data.pdbj.org/pub/pdb/validation_reports/vr/8vr0	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) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1)

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)	83.891, 101.385, 124.234
Angle α, β, γ (deg.)	90.00, 95.74, 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 KCTC 2190 (bacteria) 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-5GP / GUANOSINE-5'-MONOPHOSPHATE Mass: 363.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₈P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.43 Å³/Da / Density % sol: 49.4 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: Berkeley C10: 100 mM Sodium acetate / Hydrochloric acid pH 4.5, 100 mM Ammonium phosphate dibasic, 20% (w/v) PEG 3350, 5% (v/v) 2-Propanol, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. 10mM GMP ...Details: Berkeley C10: 100 mM Sodium acetate / Hydrochloric acid pH 4.5, 100 mM Ammonium phosphate dibasic, 20% (w/v) PEG 3350, 5% (v/v) 2-Propanol, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. 10mM GMP soak for 4 hours. Plate 13676 well C10 drop 1. Puck: PSL-0813, Cryo: 30% PEG3350 + 70% crystallant. PH range: '

Crystal

Density Matthews: 2.43 Å³/Da / Density % sol: 49.4 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Berkeley C10: 100 mM Sodium acetate / Hydrochloric acid pH 4.5, 100 mM Ammonium phosphate dibasic, 20% (w/v) PEG 3350, 5% (v/v) 2-Propanol, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. 10mM GMP ...
PH range: '

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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: 0.9785 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 9, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 2.25→47.45 Å / Num. obs: 98226 / % possible obs: 100 % / Redundancy: 6.9 % / CC_1/2: 0.991 / R_merge(I) obs: 0.266 / R_pim(I) all: 0.112 / R_rim(I) all: 0.289 / Χ²: 0.94 / Net I/σ(I): 8.8 / Num. measured all: 676252
Reflection shell	Resolution: 2.25→2.31 Å / % possible obs: 100 % / Redundancy: 7.3 % / R_merge(I) obs: 2.061 / Num. measured all: 53302 / Num. unique obs: 7270 / CC_1/2: 0.531 / R_pim(I) all: 0.82 / R_rim(I) all: 2.221 / Χ²: 0.99 / Net I/σ(I) obs: 1.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_5156: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.25→47.45 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2046	4867	4.96 %
R_work	0.1633	-	-
obs	0.1654	98183	99.93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.25→47.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14763	0	94	697	15554

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	15403
X-RAY DIFFRACTION	f_angle_d	0.822	20955
X-RAY DIFFRACTION	f_dihedral_angle_d	12.952	5732
X-RAY DIFFRACTION	f_chiral_restr	0.05	2362
X-RAY DIFFRACTION	f_plane_restr	0.008	2742

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 (%)
2.25-2.28	0.3361	156	0.2823	3108	X-RAY DIFFRACTION	100
2.28-2.3	0.2916	175	0.2509	3092	X-RAY DIFFRACTION	100
2.3-2.33	0.3028	150	0.2387	3080	X-RAY DIFFRACTION	100
2.33-2.36	0.2848	154	0.2198	3124	X-RAY DIFFRACTION	100
2.36-2.39	0.2553	147	0.226	3115	X-RAY DIFFRACTION	100
2.39-2.42	0.2518	157	0.2189	3103	X-RAY DIFFRACTION	100
2.42-2.46	0.296	149	0.2144	3069	X-RAY DIFFRACTION	100
2.46-2.5	0.274	170	0.2059	3070	X-RAY DIFFRACTION	100
2.5-2.53	0.2473	159	0.2035	3159	X-RAY DIFFRACTION	100
2.53-2.58	0.2395	179	0.2063	3062	X-RAY DIFFRACTION	100
2.58-2.62	0.2542	144	0.2028	3132	X-RAY DIFFRACTION	100
2.62-2.67	0.2115	156	0.1969	3081	X-RAY DIFFRACTION	100
2.67-2.72	0.2319	142	0.1897	3135	X-RAY DIFFRACTION	100
2.72-2.77	0.2555	169	0.1874	3067	X-RAY DIFFRACTION	100
2.77-2.83	0.2266	156	0.1852	3120	X-RAY DIFFRACTION	100
2.83-2.9	0.2892	162	0.1953	3110	X-RAY DIFFRACTION	100
2.9-2.97	0.2407	174	0.1834	3120	X-RAY DIFFRACTION	100
2.97-3.05	0.2352	165	0.1868	3096	X-RAY DIFFRACTION	100
3.05-3.14	0.2277	168	0.1875	3084	X-RAY DIFFRACTION	100
3.14-3.24	0.2274	173	0.1891	3107	X-RAY DIFFRACTION	100
3.24-3.36	0.2338	154	0.1777	3135	X-RAY DIFFRACTION	100
3.36-3.5	0.1914	169	0.1688	3104	X-RAY DIFFRACTION	100
3.5-3.65	0.1983	175	0.1596	3132	X-RAY DIFFRACTION	100
3.65-3.85	0.1727	145	0.1436	3075	X-RAY DIFFRACTION	100
3.85-4.09	0.1702	167	0.1259	3115	X-RAY DIFFRACTION	100
4.09-4.4	0.1516	192	0.112	3102	X-RAY DIFFRACTION	100
4.4-4.85	0.1347	160	0.0971	3129	X-RAY DIFFRACTION	100
4.85-5.55	0.1614	164	0.1155	3132	X-RAY DIFFRACTION	100
5.55-6.98	0.1786	168	0.1471	3165	X-RAY DIFFRACTION	100
6.98-47.45	0.1683	168	0.1501	3193	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	0.2253	-0.1421	0.0296	0.363	0.138	0.1209	-0.0321	0.0526	-0.317	-0.0881	0.0107	-0.4166	0.0811	0.2405	0.0003	0.2521	0.007	0.0721	0.301	-0.0141	0.3582	93.2567	-13.4708	19.6422
2	0.281	0.2476	-0.1639	0.47	-0.0014	0.3367	0.0055	0.0173	-0.1012	-0.0909	-0.0598	-0.0823	-0.0585	0.0295	0	0.2557	0.0108	-0.0121	0.2449	0.0059	0.2705	81.2632	-5.8739	23.7277
3	0.235	0.049	-0.0684	0.3244	0.017	0.3129	0.0239	-0.0254	0.1634	0.0082	0.0039	0.0325	-0.2103	0.057	0.0004	0.3564	-0.016	-0.0077	0.213	0.0281	0.2838	79.0293	18.5029	30.6697
4	0.0978	0.0339	-0.086	0.0265	0.0653	0.1028	-0.0264	0.0691	-0.0402	-0.0176	0.005	0.0232	-0.0526	-0.0373	0	0.2989	0.0251	-0.0029	0.2957	-0.0045	0.2889	65.91	-11.9327	21.0619
5	0.0953	-0.0919	0.1941	0.1711	-0.1937	0.4207	-0.0537	-0.0337	-0.012	0.0051	0.1468	0.4836	0.1939	-0.1906	0.0622	0.2785	-0.0583	0.1232	0.5294	0.005	0.54	19.0426	-22.7986	46.1937
6	0.0238	-0.0115	0.0125	0.0868	0.0947	0.0876	-0.0573	0.1649	-0.0904	-0.001	0.03	0.0981	0.1181	-0.2214	-0	0.3106	-0.0338	0.0227	0.3721	-0.0448	0.3329	34.1973	-24.9523	30.1248
7	0.0827	0.0992	-0.0492	0.3275	0.0342	0.1905	-0.0828	0.0585	-0.0851	0.0624	-0.008	0.0726	0.0801	-0.2011	-0	0.2569	0.0024	0.0198	0.3339	-0.0071	0.3197	37.2493	-20.0882	38.3587
8	0.0773	0.0622	0.0141	0.0562	0.0784	0.1165	0.017	-0.1504	0.009	0.0296	0.0074	0.0631	-0.0276	-0.0256	0	0.3063	0.0412	0.0686	0.3372	-0.013	0.3317	43.8761	-8.9649	53.8604
9	0.2603	-0.0965	0.0606	0.2983	0.0259	0.253	0.0056	-0.2579	0.1398	0.3065	-0.1065	0.3091	-0.1004	-0.1834	-0.1408	0.3815	0.0667	0.1254	0.4401	-0.0777	0.4188	33.6074	2.3247	61.8971
10	0.3372	0.0623	-0.0221	0.0993	0.1751	0.2863	-0.0399	-0.1405	-0.0603	0.1183	-0.0118	0.1094	0.0752	-0.0897	0	0.3009	0.0247	0.0213	0.2943	0.0138	0.2408	51.0249	-9.6218	51.605
11	0.0395	-0.0164	-0.0205	0.1484	0.0213	0.0131	-0.0033	0.2514	0.1153	-0.1863	0.0171	0.1141	-0.0731	-0.1145	0.0042	0.539	0.3081	-0.0474	0.6427	0.1599	0.2584	45.5678	4.0976	-6.433
12	0.0713	-0.053	-0.036	0.0603	0.0774	0.0979	0.0596	0.0746	0.1237	-0.0131	-0.0754	0.0603	-0.2233	-0.345	-0.0027	0.3094	0.0787	0.0036	0.3257	0.0125	0.2628	46.2626	2.3106	15.6063
13	0.3691	-0.0178	-0.3384	0.2138	0.061	0.2728	0.0625	0.1767	-0.0393	-0.0112	-0.0494	0.0019	-0.1291	-0.2675	0.0012	0.2196	0.0836	-0.0456	0.3346	-0.0054	0.172	50.1478	-5.6001	11.2564
14	0.2374	-0.1661	-0.1032	0.1299	0.026	0.142	0.112	0.2634	-0.0295	-0.0064	-0.1512	-0.0499	-0.0604	-0.1592	-0.0107	0.3391	0.0014	-0.0043	0.3936	-0.1006	0.2886	61.3518	-14.0113	2.2297
15	0.1133	0.0107	-0.0081	0.0351	-0.0132	0.0787	-0.035	0.3541	-0.3024	-0.2577	-0.0126	0.0963	0.0278	-0.4148	-0.1406	0.3714	-0.026	-0.0647	0.6831	-0.3804	0.1741	55.1029	-26.922	-13.2995
16	0.46	-0.0192	-0.035	0.0694	-0.0188	0.3235	0.0223	0.168	-0.1748	-0.0211	-0.0212	-0.0152	0.0033	-0.0415	-0.0082	0.276	0.0118	-0.0059	0.3071	-0.0825	0.2896	64.905	-21.4354	7.4386
17	0.2904	-0.1962	0.035	0.3044	0.1741	0.3057	0.0114	-0.5171	-0.2587	0.099	-0.007	-0.0333	0.1139	0.0059	0.2668	0.342	0.0599	-0.0433	0.4522	0.2087	0.3812	75.7485	-32.7665	56.337
18	0.7234	0.1147	0.0882	0.2223	-0.1083	0.3668	0.0318	-0.382	-0.324	0.0158	0.0269	0.04	0.0953	-0.1298	-0.0521	0.2935	0.0152	-0.003	0.2878	0.1539	0.3684	64.3425	-31.2301	47.2568
19	0.106	-0.0527	0.0467	0.0268	-0.0317	0.0552	0.0693	-0.1348	-0.5134	0.0522	0.0013	0.0163	0.4305	-0.104	-0.0541	0.6581	-0.0952	-0.0875	0.308	0.1803	0.897	61.235	-58.088	39.6729
20	0.3507	0.0832	0.029	0.1496	-0.0673	0.1411	-0.0831	-0.1069	-0.2055	0.1827	0.1092	0.1177	0.1012	-0.0645	-0.0014	0.3019	-0.006	0.0288	0.2399	0.0733	0.3869	55.8466	-29.0254	35.4257

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 290 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 291 through 441 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 442 through 490 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 42 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 43 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 211 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 212 through 290 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 291 through 363 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 364 through 490 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 4 through 104 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 105 through 290 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 291 through 409 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 410 through 490 )

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