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

ID or keywords:

Entry

Database: PDB / ID: 8vqw

Title

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (CoA 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: 2.2 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 (CoA 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	8vqw.cif.gz	752.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8vqw.ent.gz	621.9 KB	Display	PDB format
PDBx/mmJSON format	8vqw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vqw_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8vqw_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8vqw_validation.xml.gz	71.3 KB	Display
Data in CIF	8vqw_validation.cif.gz	100.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vq/8vqw ftp://data.pdbj.org/pub/pdb/validation_reports/vq/8vqw	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) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor 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)	83.818, 101.008, 123.928
Angle α, β, γ (deg.)	90.00, 95.94, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#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

#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

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Non-polymers , 6 types, 676 molecules

#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 670 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.41 Å³/Da / Density % sol: 49.02 %
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 FAD ...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 FAD soak for 4 hours. Plate 13676 well C10 drop 1. Puck: PSL-0807, Cryo: 30% PEG3350 + 70% crystallant.

Crystal

Density Matthews: 2.41 Å³/Da / Density % sol: 49.02 %

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 FAD ...

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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: 2.2→47.27 Å / Num. obs: 104242 / % possible obs: 99.9 % / Redundancy: 7 % / CC_1/2: 0.997 / R_merge(I) obs: 0.143 / R_pim(I) all: 0.058 / R_rim(I) all: 0.155 / Χ²: 1.01 / Net I/σ(I): 9.4 / Num. measured all: 734621
Reflection shell	Resolution: 2.2→2.26 Å / % possible obs: 100 % / Redundancy: 7.4 % / R_merge(I) obs: 1.282 / Num. measured all: 56861 / Num. unique obs: 7708 / CC_1/2: 0.678 / R_pim(I) all: 0.504 / R_rim(I) all: 1.379 / Χ²: 1.01 / Net I/σ(I) obs: 1.6

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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: 2.2→47.27 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2033	5118	4.91 %
R_work	0.1603	-	-
obs	0.1624	104186	99.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→47.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14761	0	120	670	15551

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	15348
X-RAY DIFFRACTION	f_angle_d	0.839	20869
X-RAY DIFFRACTION	f_dihedral_angle_d	14.473	5735
X-RAY DIFFRACTION	f_chiral_restr	0.05	2347
X-RAY DIFFRACTION	f_plane_restr	0.007	2727

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 (%)
2.2-2.23	0.2963	170	0.2545	3311	X-RAY DIFFRACTION	100
2.23-2.25	0.3067	191	0.251	3264	X-RAY DIFFRACTION	100
2.25-2.28	0.2791	176	0.2321	3252	X-RAY DIFFRACTION	100
2.28-2.31	0.2861	165	0.2278	3302	X-RAY DIFFRACTION	100
2.31-2.34	0.2899	168	0.2159	3303	X-RAY DIFFRACTION	100
2.34-2.37	0.2824	157	0.2119	3274	X-RAY DIFFRACTION	100
2.37-2.4	0.2594	183	0.209	3281	X-RAY DIFFRACTION	100
2.4-2.44	0.2729	168	0.2039	3291	X-RAY DIFFRACTION	100
2.44-2.48	0.2694	177	0.2008	3332	X-RAY DIFFRACTION	100
2.48-2.52	0.2576	176	0.1895	3256	X-RAY DIFFRACTION	100
2.52-2.56	0.2395	149	0.1905	3268	X-RAY DIFFRACTION	100
2.56-2.61	0.237	156	0.1884	3349	X-RAY DIFFRACTION	100
2.61-2.66	0.2667	182	0.1861	3272	X-RAY DIFFRACTION	100
2.66-2.71	0.2888	166	0.1918	3302	X-RAY DIFFRACTION	100
2.71-2.77	0.252	178	0.1922	3290	X-RAY DIFFRACTION	100
2.77-2.84	0.2172	197	0.1828	3263	X-RAY DIFFRACTION	100
2.84-2.91	0.2024	177	0.1786	3329	X-RAY DIFFRACTION	100
2.91-2.99	0.1941	192	0.1731	3242	X-RAY DIFFRACTION	100
2.99-3.07	0.248	162	0.183	3306	X-RAY DIFFRACTION	100
3.07-3.17	0.2259	185	0.1887	3297	X-RAY DIFFRACTION	100
3.17-3.29	0.2614	150	0.1904	3307	X-RAY DIFFRACTION	100
3.29-3.42	0.2087	155	0.1736	3322	X-RAY DIFFRACTION	100
3.42-3.57	0.2009	163	0.1625	3299	X-RAY DIFFRACTION	100
3.57-3.76	0.2026	165	0.1504	3329	X-RAY DIFFRACTION	100
3.76-4	0.1765	186	0.1371	3305	X-RAY DIFFRACTION	100
4-4.31	0.1416	178	0.114	3266	X-RAY DIFFRACTION	100
4.31-4.74	0.1256	183	0.0983	3327	X-RAY DIFFRACTION	100
4.74-5.42	0.1297	155	0.1104	3337	X-RAY DIFFRACTION	100
5.42-6.83	0.1825	149	0.1428	3378	X-RAY DIFFRACTION	100
6.83-47.27	0.1738	159	0.1407	3414	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	0.3126	-0.2375	0.0861	1.0455	0.5001	0.3536	-0.0378	0.0438	-0.2787	-0.1395	-0.0021	-0.3384	0.1167	0.2875	-0.002	0.2509	0.0213	0.0087	0.3451	-0.0158	0.3091	93.2754	-13.473	19.7626
2	0.5724	0.45	-0.2423	0.6671	-0.0489	0.5711	-0.0529	0.0486	-0.0407	-0.0668	0.0077	-0.0558	-0.0233	0.0692	0	0.26	0.0164	-0.0214	0.2578	0.0019	0.2796	82.0999	-9.4552	21.3646
3	0.7832	0.3253	0.0109	0.5426	0.0192	0.5501	0.0863	-0.0643	0.1717	-0.0217	-0.0381	0.0332	-0.2151	0.0829	-0	0.3274	-0.0246	0.0165	0.2179	0.0015	0.272	81.3878	19.3868	31.3656
4	0.4076	0.3247	-0.1043	0.115	0.2921	0.3492	0.0169	0.0841	0.0196	-0.0669	-0.0064	0.0313	-0.1013	-0.0693	0.0003	0.2999	0.0239	-0.0234	0.2448	0.0049	0.2667	65.3337	-3.3796	25.5553
5	0.2545	0.2145	0.1886	0.1809	0.1318	0.1006	-0.1458	0.1897	0.0036	0.0336	-0.152	0.7529	0.2036	-0.3176	-0.0019	0.2873	-0.0359	0.0868	0.4416	-0.0271	0.5216	18.8032	-23.0221	45.8538
6	0.2668	-0.0187	0.1552	0.2841	0.2308	0.2804	-0.0585	0.163	-0.1605	-0.2635	0.0028	0.0651	0.1795	-0.2113	0	0.2946	-0.0068	0.001	0.3216	-0.0352	0.3392	34.0464	-24.9608	29.8446
7	0.3245	0.0236	-0.4525	0.4589	0.2577	0.4052	-0.0406	-0.0191	-0.0102	0.0087	-0.0057	0.019	0.0351	-0.121	-0	0.2403	0.0184	-0.0138	0.3128	-0.0034	0.2964	36.9394	-20.1441	38.1618
8	0.1544	0.0605	-0.2851	0.2407	0.2101	0.1225	0.0583	-0.1683	0.0185	0.164	0.0072	0.0384	-0.028	0.0606	-0	0.3203	0.0364	0.0135	0.3582	0.001	0.3136	43.6208	-9.081	53.6566
9	0.3542	-0.0066	-0.0317	0.5773	0.6068	0.5319	-0.0033	-0.2166	0.2465	0.198	-0.1079	0.2625	-0.1268	-0.2339	-0.0044	0.3592	0.0224	0.0718	0.4381	-0.0346	0.3578	33.2829	2.0831	61.7416
10	0.5987	-0.1007	-0.3161	0.1703	0.3939	0.5928	-0.0385	-0.1676	-0.0582	0.0872	-0.0264	0.0907	0.0545	-0.006	0	0.282	0.0074	0.0035	0.3014	0.0102	0.2432	50.6963	-9.7409	51.3271
11	0.8991	-0.0409	0.141	0.8412	0.2029	0.4721	0.1564	0.2626	0.2477	-0.0755	-0.1345	0.1145	-0.3453	-0.4001	0.0418	0.3312	0.1383	-0.0249	0.4066	0.043	0.2775	45.7757	3.3331	4.8067
12	0.4313	-0.0162	-0.3719	0.3244	0.1688	0.6852	0.0191	0.2107	-0.0258	-0.04	-0.0164	-0.0177	-0.102	-0.1912	0.0003	0.2368	0.0394	-0.0338	0.3495	-0.0228	0.215	54.1249	-8.6372	7.7149
13	0.2014	-0.0199	-0.4494	1.2221	0.1923	1.0124	-0.0664	0.2908	-0.2003	-0.1935	0.0125	-0.0983	0.0848	-0.2694	-0.2456	0.3338	-0.0427	0.0015	0.4945	-0.1481	0.3078	59.3086	-27.2838	-11.0903
14	0.3617	-0.0318	-0.0772	0.0831	0.1158	0.5889	-0.0337	0.0806	-0.0809	-0.0716	-0.025	0.0295	-0.0575	-0.068	-0	0.2673	-0.0026	0.0009	0.2906	-0.0304	0.282	64.3874	-17.4908	16.4513
15	0.4823	-0.1095	0.2487	0.1515	0.1131	0.3188	-0.1312	-0.5744	-0.0587	0.2099	0.084	-0.0258	0.1788	0.0051	-0.1693	0.4786	0.0893	-0.0074	0.5982	0.1541	0.3155	72.2203	-32.2895	64.0458
16	0.6799	0.1145	-0.0768	0.2526	-0.1317	0.5883	-0.001	-0.2506	-0.2677	0.0273	-0.0308	-0.0121	0.1099	-0.0087	-0.0032	0.2908	0.0386	0.002	0.2796	0.0867	0.3445	67.454	-31.5282	46.9874
17	0.3175	-0.0411	-0.0193	0.4258	-0.2164	0.5751	0.0081	-0.0659	-0.4252	0.0004	0.0041	-0.0346	0.4078	-0.0759	-0.1314	0.5968	-0.0499	0.0215	0.2912	0.0522	0.6358	61.2755	-57.9766	39.6941
18	0.2483	0.1011	0.0954	0.3007	0.0684	0.2134	-0.05	-0.0145	-0.1031	0.1882	0.0575	0.0511	0.1116	-0.0934	-0	0.3034	-0.0077	0.0307	0.2516	0.0364	0.3428	55.7709	-28.9604	35.3203

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 257 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 258 through 409 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 410 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 81 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 82 through 290 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 291 through 409 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 410 through 490 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 4 through 62 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 63 through 290 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 291 through 409 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 410 through 490 )

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