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

ID or keywords:

Entry

Database: PDB / ID: 8uzm

Title

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (NADPH 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: 2.2 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 (NADPH 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	8uzm.cif.gz	759 KB	Display	PDBx/mmCIF format
PDB format	pdb8uzm.ent.gz	630 KB	Display	PDB format
PDBx/mmJSON format	8uzm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8uzm_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	8uzm_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8uzm_validation.xml.gz	71 KB	Display
Data in CIF	8uzm_validation.cif.gz	98.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uz/8uzm ftp://data.pdbj.org/pub/pdb/validation_reports/uz/8uzm	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) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Betaine aldehyde dehydrogenase

B: Betaine aldehyde dehydrogenase

C: Betaine aldehyde dehydrogenase

D: Betaine aldehyde dehydrogenase

hetero molecules

219 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)	84.096, 100.798, 123.675
Angle α, β, γ (deg.)	90.00, 95.79, 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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.41 Å³/Da / Density % sol: 49 %
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 5mM NADPH in crystallant. Puck: PSL-0503, 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: 2.2→123.04 Å / Num. obs: 104034 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC_1/2: 0.994 / R_merge(I) obs: 0.14 / R_pim(I) all: 0.084 / R_rim(I) all: 0.163 / Χ²: 0.84 / Net I/σ(I): 8.3 / Num. measured all: 391626
Reflection shell	Resolution: 2.2→2.26 Å / % possible obs: 99.9 % / Redundancy: 3.9 % / R_merge(I) obs: 1.187 / Num. measured all: 30218 / Num. unique obs: 7684 / CC_1/2: 0.5 / R_pim(I) all: 0.695 / R_rim(I) all: 1.379 / Χ²: 0.75 / Net I/σ(I) obs: 1.5

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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: 2.2→83.67 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2175	5117	4.92 %
R_work	0.1719	-	-
obs	0.1741	103945	99.68 %

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→83.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14790	0	195	599	15584

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	15562
X-RAY DIFFRACTION	f_angle_d	0.904	21204
X-RAY DIFFRACTION	f_dihedral_angle_d	13.225	5822
X-RAY DIFFRACTION	f_chiral_restr	0.054	2395
X-RAY DIFFRACTION	f_plane_restr	0.008	2766

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 (%)
2.2-2.22	0.3209	182	0.2827	3292	X-RAY DIFFRACTION	100
2.23-2.25	0.3222	192	0.27	3254	X-RAY DIFFRACTION	100
2.25-2.28	0.2969	179	0.2577	3272	X-RAY DIFFRACTION	100
2.28-2.31	0.3094	155	0.2498	3272	X-RAY DIFFRACTION	100
2.31-2.34	0.2729	174	0.2413	3339	X-RAY DIFFRACTION	100
2.34-2.37	0.3222	156	0.2305	3234	X-RAY DIFFRACTION	100
2.37-2.4	0.2961	179	0.2404	3309	X-RAY DIFFRACTION	100
2.4-2.44	0.2771	174	0.2256	3260	X-RAY DIFFRACTION	100
2.44-2.48	0.2828	169	0.2236	3330	X-RAY DIFFRACTION	100
2.48-2.52	0.2814	184	0.2137	3258	X-RAY DIFFRACTION	100
2.52-2.56	0.2812	142	0.2096	3296	X-RAY DIFFRACTION	100
2.56-2.61	0.2694	165	0.202	3308	X-RAY DIFFRACTION	100
2.61-2.66	0.2485	175	0.1973	3289	X-RAY DIFFRACTION	100
2.66-2.71	0.2709	164	0.1953	3294	X-RAY DIFFRACTION	100
2.71-2.77	0.2314	183	0.1936	3256	X-RAY DIFFRACTION	100
2.77-2.84	0.2641	196	0.1931	3283	X-RAY DIFFRACTION	100
2.84-2.91	0.2291	177	0.1976	3301	X-RAY DIFFRACTION	100
2.91-2.99	0.2403	183	0.1822	3245	X-RAY DIFFRACTION	100
2.99-3.07	0.2517	169	0.1883	3292	X-RAY DIFFRACTION	100
3.07-3.17	0.2382	180	0.1925	3297	X-RAY DIFFRACTION	100
3.17-3.29	0.2612	150	0.185	3303	X-RAY DIFFRACTION	100
3.29-3.42	0.2221	160	0.1825	3273	X-RAY DIFFRACTION	99
3.42-3.57	0.2114	159	0.1722	3326	X-RAY DIFFRACTION	100
3.57-3.76	0.2166	164	0.1603	3292	X-RAY DIFFRACTION	99
3.76-4	0.1657	178	0.1417	3274	X-RAY DIFFRACTION	98
4-4.31	0.1797	183	0.1258	3278	X-RAY DIFFRACTION	100
4.31-4.74	0.129	182	0.1049	3311	X-RAY DIFFRACTION	100
4.74-5.43	0.1464	156	0.1241	3332	X-RAY DIFFRACTION	100
5.43-6.83	0.1847	147	0.1593	3362	X-RAY DIFFRACTION	100
6.84-83.67	0.1848	160	0.1435	3396	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	0.2984	-0.0405	0.0047	0.5884	0.3222	0.231	0.0504	0.0525	-0.2492	-0.1057	-0.0393	-0.2934	0.1352	0.306	0.0122	0.2506	0.0248	0.0568	0.3209	-0.0083	0.2988	93.7959	-13.424	19.4868
2	0.1624	0.1984	-0.2047	0.3465	-0.1234	0.6951	0.0205	-0.0078	-0.131	-0.0621	-0.0241	-0.1278	0.0153	0.1296	0	0.2143	0.0196	0.0089	0.2491	-0.0095	0.2736	83.7365	-11.2073	23.6716
3	0.277	0.0135	-0.0511	0.3939	-0.1993	0.0984	0.0305	0.0019	0.0365	-0.1051	-0.0718	0.2082	-0.0486	-0.0143	0	0.2778	-0.0176	-0.0195	0.233	-0.0144	0.2334	77.4416	5.3766	23.3373
4	0.5221	0.0399	-0.1434	0.4054	0.1235	0.5213	0.0651	-0.0707	0.1318	0.0135	-0.0224	0.0057	-0.1962	0.1038	0	0.3165	-0.0233	0.0022	0.2108	0.0097	0.2732	79.2757	18.4554	30.5618
5	0.0618	0.1012	-0.1009	-0.0048	0.108	0.4023	-0.054	0.0718	0.0142	-0.0648	0.0386	0.051	-0.0828	-0.0527	-0	0.2886	-0.003	-0.0141	0.2904	-0.0165	0.2926	66.2287	-11.7109	20.7406
6	0.2078	0.2117	0.112	0.6426	0.1775	0.4197	0.0066	0.1534	-0.0095	-0.1102	0.0655	0.2674	0.1903	-0.2359	0.0466	0.2081	-0.0277	0.0192	0.2708	0.0265	0.317	26.7534	-24.1917	37.677
7	0.1877	0.0552	-0.2123	0.3166	0.1282	0.2583	-0.0152	-0.0601	0.0284	0.0286	0.0264	0.0172	0.0146	-0.0959	0.0001	0.2401	-0.0038	0.0056	0.2959	-0.0005	0.2651	37.2383	-20.0695	38.0896
8	0.2475	0.1347	-0.1094	0.1407	0.0952	0.2356	0.1095	-0.1422	0.06	0.0662	-0.0227	-0.0628	-0.0307	0.1749	-0.0001	0.251	0.0548	0.0027	0.3	-0.0103	0.2832	44.1369	-9.1387	53.4311
9	0.2225	0.0376	0.0374	0.2725	0.348	0.5914	0.0504	-0.2492	0.2083	0.1755	-0.0651	0.088	-0.0567	-0.0886	-0.0001	0.2911	0.0288	0.056	0.3956	-0.0386	0.3082	37.6993	0.6609	62.7024
10	0.0601	-0.0473	-0.0998	0.1946	0.3324	0.2931	-0.0521	-0.095	-0.0611	0.0909	0.0466	0.0974	0.054	-0.0118	0	0.2414	0.0092	-0.0013	0.2624	0.0123	0.2483	55.1481	-14.3159	43.556
11	0.1694	-0.04	-0.1807	0.1529	0.2341	0.4594	0.245	0.3855	0.2903	-0.4515	-0.226	0.0603	-0.4163	-0.3563	-0.0137	0.4807	0.1946	0.0154	0.5102	0.1526	0.3188	45.5944	4.03	-6.9395
12	0.1952	-0.123	-0.046	0.2319	0.2464	0.2731	0.1048	0.0126	0.2485	0.1583	0.0105	0.0903	-0.1493	-0.3133	-0.0018	0.2949	0.0498	0.0247	0.2693	0.0053	0.3611	46.4786	2.5813	15.1612
13	0.3419	-0.0954	-0.2604	0.0743	0.1154	0.2293	0.052	0.0963	0.0468	0.0153	-0.114	0.0015	0.0639	-0.1423	-0	0.2168	0.0129	-0.019	0.284	-0.0028	0.2134	50.9909	-8.5873	13.5051
14	0.4667	-0.0129	-0.4457	0.4342	0.0497	0.5408	0.0818	0.2675	0.0452	-0.1213	0.0376	-0.1213	-0.0382	-0.1548	0.0007	0.2333	0.0212	-0.0154	0.3158	-0.0182	0.2741	56.8954	-8.9027	2.8901
15	0.2447	0.077	-0.3708	0.5015	0.2513	0.7997	0.0037	0.3345	-0.218	-0.1536	0.003	-0.1123	0.1561	-0.1709	-0.0538	0.3034	-0.0162	0.0101	0.3897	-0.107	0.2754	60.6112	-27.9988	-7.2794
16	0.2963	0.1435	-0.1151	0.0586	0.011	0.1459	-0.058	-0.0056	-0.0662	-0.0437	-0.0368	0.0934	-0.0622	-0.0357	-0.0008	0.2581	-0.0101	-0.013	0.2792	-0.0058	0.2292	64.0954	-9.3013	21.077
17	0.4447	-0.2261	0.2292	0.596	0.2972	0.8042	0.0394	-0.5443	-0.0141	0.2406	-0.0306	-0.1469	0.0866	-0.0035	0.1268	0.3225	0.0123	-0.0297	0.5018	0.1422	0.2689	74.7456	-29.7282	58.9079
18	0.5256	-0.0164	0.0632	0.353	0.0805	0.4226	0.0962	-0.3728	-0.1213	-0.0313	-0.0118	-0.0224	0.119	-0.0837	0.0528	0.2307	0.0032	-0.0327	0.3003	0.1194	0.245	67.9425	-29.0243	50.0724
19	0.2455	-0.0564	0.3157	0.0347	-0.186	1.072	0.2463	-0.29	-0.2702	0.0743	0.0048	-0.0697	0.8078	-0.5894	0.1384	0.6517	-0.1437	-0.1286	0.1039	0.1275	0.5272	60.5022	-50.9148	36.8078
20	0.0613	0.0132	0.0271	-0.0005	0.0083	-0.0041	-0.0692	-0.0642	-0.1225	0.1638	0.0929	0.2641	-0.0429	-0.0755	0	0.3164	0.0486	0.0022	0.289	0.039	0.3315	53.1446	-6.8295	43.5418

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 218 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 219 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 409 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 410 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 168 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 169 through 290 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 291 through 441 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 442 through 490 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 3 through 81 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 82 through 244 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 245 through 465 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 466 through 490 )

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