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

ID or keywords:

Entry

Database: PDB / ID: 8vqz

Title

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (CMP 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: 2.05 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 (CMP 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	8vqz.cif.gz	760.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8vqz.ent.gz	629.3 KB	Display	PDB format
PDBx/mmJSON format	8vqz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vqz_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8vqz_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8vqz_validation.xml.gz	72.9 KB	Display
Data in CIF	8vqz_validation.cif.gz	104.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vq/8vqz ftp://data.pdbj.org/pub/pdb/validation_reports/vq/8vqz	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)	84.048, 101.329, 123.914
Angle α, β, γ (deg.)	90.00, 96.05, 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-C5P / CYTIDINE-5'-MONOPHOSPHATE Mass: 323.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₄N₃O₈P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 822 / 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: 49.31 %
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 CMP ...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 CMP soak for 4 hours. Plate 13676 well C10 drop 1. Puck: PSL-0811, Cryo: 30% PEG3350 + 70% crystallant.

Crystal

Density Matthews: 2.43 Å³/Da / Density % sol: 49.31 %

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 CMP ...

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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: 2.05→47.27 Å / Num. obs: 129364 / % possible obs: 99.9 % / Redundancy: 7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.108 / R_pim(I) all: 0.044 / R_rim(I) all: 0.117 / Χ²: 1.02 / Net I/σ(I): 10.9 / Num. measured all: 904139
Reflection shell	Resolution: 2.05→2.1 Å / % possible obs: 100 % / Redundancy: 6.9 % / R_merge(I) obs: 1.233 / Num. measured all: 65527 / Num. unique obs: 9541 / CC_1/2: 0.689 / R_pim(I) all: 0.506 / R_rim(I) all: 1.334 / Χ²: 1.05 / Net I/σ(I) obs: 1.7

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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: 2.05→47.27 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1905	6466	5 %
R_work	0.1603	-	-
obs	0.1618	129273	99.86 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.05→47.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14750	0	114	822	15686

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	15375
X-RAY DIFFRACTION	f_angle_d	0.831	20917
X-RAY DIFFRACTION	f_dihedral_angle_d	12.935	5698
X-RAY DIFFRACTION	f_chiral_restr	0.052	2361
X-RAY DIFFRACTION	f_plane_restr	0.008	2734

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 (%)
2.05-2.07	0.3177	206	0.2679	4032	X-RAY DIFFRACTION	100
2.07-2.1	0.2906	216	0.2507	4124	X-RAY DIFFRACTION	100
2.1-2.12	0.3093	204	0.2456	4060	X-RAY DIFFRACTION	100
2.12-2.15	0.2909	236	0.2406	4078	X-RAY DIFFRACTION	100
2.15-2.18	0.2647	226	0.2341	4031	X-RAY DIFFRACTION	100
2.18-2.21	0.2311	218	0.2189	4105	X-RAY DIFFRACTION	100
2.21-2.24	0.2684	201	0.2185	4067	X-RAY DIFFRACTION	100
2.24-2.27	0.2669	225	0.2168	4086	X-RAY DIFFRACTION	100
2.27-2.31	0.2793	200	0.2094	4132	X-RAY DIFFRACTION	100
2.31-2.35	0.2169	220	0.1946	4039	X-RAY DIFFRACTION	100
2.35-2.39	0.231	217	0.1794	4102	X-RAY DIFFRACTION	100
2.39-2.43	0.2143	216	0.1757	4054	X-RAY DIFFRACTION	100
2.43-2.48	0.2288	211	0.1785	4128	X-RAY DIFFRACTION	100
2.48-2.53	0.2127	230	0.1712	4087	X-RAY DIFFRACTION	100
2.53-2.58	0.2194	190	0.1702	4105	X-RAY DIFFRACTION	100
2.58-2.64	0.2222	244	0.1778	4036	X-RAY DIFFRACTION	100
2.64-2.71	0.221	192	0.1818	4132	X-RAY DIFFRACTION	100
2.71-2.78	0.2458	212	0.1832	4068	X-RAY DIFFRACTION	100
2.78-2.86	0.2341	230	0.1856	4097	X-RAY DIFFRACTION	100
2.86-2.96	0.2297	223	0.1757	4084	X-RAY DIFFRACTION	100
2.96-3.06	0.2249	214	0.1759	4108	X-RAY DIFFRACTION	100
3.06-3.18	0.2341	200	0.182	4092	X-RAY DIFFRACTION	100
3.18-3.33	0.2063	217	0.1831	4096	X-RAY DIFFRACTION	100
3.33-3.51	0.1836	233	0.1676	4095	X-RAY DIFFRACTION	100
3.51-3.72	0.171	194	0.153	4108	X-RAY DIFFRACTION	99
3.72-4.01	0.1702	213	0.1324	4098	X-RAY DIFFRACTION	100
4.01-4.42	0.1358	193	0.1132	4109	X-RAY DIFFRACTION	99
4.42-5.05	0.1163	217	0.1005	4136	X-RAY DIFFRACTION	100
5.05-6.36	0.1473	232	0.1295	4123	X-RAY DIFFRACTION	100
6.37-47.27	0.1459	236	0.1433	4195	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	0.3733	-0.175	-0.0012	0.7218	0.4242	0.1139	-0.0426	0.0606	-0.2597	-0.1119	-0.0128	-0.3735	0.0932	0.3156	-0	0.308	0.0204	0.0387	0.3954	0.0062	0.3821	93.2321	-13.6426	19.5226
2	0.5736	0.3038	-0.2882	0.735	-0.0294	0.3993	-0.0249	0.0319	-0.0663	-0.0992	-0.0295	-0.073	-0.0377	0.047	0	0.2909	0.0185	-0.0224	0.2921	0.0042	0.281	81.3197	-5.9254	23.6675
3	0.6531	0.2159	-0.2444	0.576	0.0248	0.4693	0.0956	-0.0083	0.2445	-0.0058	-0.0039	0.0277	-0.2459	0.0804	0	0.4005	-0.0209	0.0113	0.2619	0.0218	0.3252	78.9907	18.3357	30.6462
4	0.3089	0.0204	-0.3595	-0.0515	0.1069	0.2873	-0.0434	0.1417	-0.0976	-0.0205	0.0108	0.0018	-0.0828	-0.0887	0	0.3276	0.0248	-0.0265	0.3294	-0.0109	0.3095	65.8652	-12.0405	20.9027
5	0.1045	0.1788	-0.0146	0.0402	0.0859	-0.0123	-0.0065	0.0984	-0.0765	0.0739	-0.1085	0.5596	0.1186	-0.3179	0	0.3405	-0.0378	0.0842	0.5255	-0.0133	0.5745	18.8117	-23.0429	45.8357
6	0.1164	-0.0479	0.0294	0.1289	0.1862	0.1568	-0.0633	0.273	-0.1666	-0.1702	0.0081	0.0417	0.1858	-0.2353	0	0.3425	-0.0216	0.0045	0.4081	-0.0645	0.4004	34.0542	-25.0281	29.7863
7	0.2802	0.0902	-0.3058	0.4705	0.157	0.4746	-0.107	0.0149	-0.127	0.0835	0.0082	0.0816	0.0946	-0.1505	-0	0.2788	0.0115	-0.0031	0.3415	-0.0075	0.3369	37.0597	-20.2447	38.0937
8	0.3769	0.2479	-0.2219	0.0834	0.2359	0.3545	0.0214	-0.1061	-0.0332	0.0323	-0.0222	0.045	0.0098	-0.0252	-0	0.3439	0.0353	0.0221	0.3433	-0.0004	0.3396	43.7049	-8.9519	53.6131
9	0.304	-0.1525	-0.0315	0.333	0.5014	0.3528	-0.0038	-0.2743	0.1927	0.2206	-0.1039	0.2863	-0.1437	-0.1491	-0	0.3814	0.0472	0.0832	0.4375	-0.0402	0.404	33.3377	2.076	61.7362
10	0.602	-0.0132	-0.3186	0.3153	0.3326	0.5352	-0.05	-0.1642	-0.0803	0.1111	-0.0148	0.1056	0.0546	-0.0266	0	0.3318	0.0339	0.003	0.3162	0.0274	0.2709	50.7957	-9.8078	51.4227
11	0.2878	-0.2297	-0.0306	0.1539	0.1449	0.1436	0.1201	0.4802	0.0975	-0.2081	-0.2566	0.0947	-0.2872	-0.5592	-0.0179	0.5535	0.2383	-0.0168	0.7416	0.129	0.3531	45.804	4.2367	-6.4483
12	0.2119	-0.1592	-0.0985	0.1536	0.2529	0.1726	0.1302	0.0775	0.2222	0.0898	-0.106	0.0747	-0.2785	-0.2983	-0	0.3569	0.0815	-0.0144	0.405	0.026	0.3414	46.1072	2.1935	15.524
13	0.7098	-0.0209	-0.4462	0.3181	0.33	0.6159	0.0317	0.2975	-0.0756	-0.0401	-0.0404	-0.0454	-0.1013	-0.1947	-0.0432	0.2456	0.0481	-0.0348	0.3573	-0.0328	0.1933	54.2397	-8.7187	7.7869
14	0.1717	-0.1038	-0.2165	0.6691	0.2989	0.6569	-0.1221	0.3813	-0.3392	-0.2079	-0.0029	-0.0724	-0.0251	-0.3288	-0.3153	0.3766	-0.0228	0.0025	0.6496	-0.2391	0.3399	59.2705	-27.2883	-11.3223
15	0.3224	-0.0008	-0.0927	0.0288	0.1458	0.4362	-0.0683	0.1198	-0.1384	-0.0256	0.0148	-0.0343	-0.0437	-0.0046	-0	0.2969	-0.0028	-0.0037	0.3234	-0.0553	0.3202	64.4261	-17.613	16.3874
16	0.789	-0.0551	0.2616	0.4944	0.5118	0.631	-0.0896	-0.5718	-0.3966	0.1318	-0.0026	-0.1231	0.2292	0.0857	0.0236	0.3829	0.1145	0.0284	0.51	0.2454	0.4473	75.4387	-32.8197	56.371
17	1.1741	-0.0448	-0.0472	0.074	-0.1577	0.5535	-0.1001	-0.3868	-0.4477	0.0497	0.0128	0.0291	0.1215	-0.0427	-0.1576	0.3074	0.0577	0.0504	0.2926	0.1598	0.4077	64.1816	-31.3536	47.006
18	0.3529	-0.0939	0.2194	0.1858	0.0294	0.2189	-0.2077	-0.1533	-1.1651	0.1498	0.0872	0.2661	0.6304	-0.1027	-0.3847	0.6922	-0.0411	0.2376	0.1296	0.2875	1.3451	61.0312	-58.2414	39.4383
19	0.4812	-0.0563	-0.0723	0.7514	0.1243	0.3363	-0.1994	-0.122	-0.3008	0.2379	0.1043	0.2157	0.1145	-0.0191	-0.0224	0.2677	0.0004	0.0687	0.2188	0.0613	0.4299	55.6991	-29.1288	35.192

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 4 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 290 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 291 through 409 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 410 through 490 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 4 through 104 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 105 through 290 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 291 through 409 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 410 through 490 )

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