PDB-6wsb: Crystal structure of a betaine aldehyde dehydrogenase from Burkho...

ID or keywords:

Entry

Database: PDB / ID: 6wsb

Title

Crystal structure of a betaine aldehyde dehydrogenase from Burkholderia pseudomallei bound to cofactor NAD

Components

NAD/NADP-dependent betaine aldehyde dehydrogenase

Keywords

OXIDOREDUCTASE / National Institute of Allergy and Infectious Diseases / NIAID / structural genomics / melioidosis / glycine metabolism / serine metabolism / threonine metabolism / covalently bound cofactor / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / : / metal ion binding
Similarity search - Function

Biological species

Burkholderia pseudomallei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structure of betaine aldehyde dehydrogenase from Burkholderia pseudomallei.
Authors: Beard, D.K. / Subramanian, S. / Abendroth, J. / Dranow, D.M. / Edwards, T.E. / Myler, P.J. / Asojo, O.A.

History

Deposition	Apr 30, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 20, 2020	Provider: repository / Type: Initial release
Revision 1.1	Feb 16, 2022	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Dec 25, 2024	Group: Advisory / Derived calculations / Structure summary Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6wsb.cif.gz	409.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6wsb.ent.gz	331 KB	Display	PDB format
PDBx/mmJSON format	6wsb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ws/6wsb ftp://data.pdbj.org/pub/pdb/validation_reports/ws/6wsb	HTTPS FTP

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Related structure data

Related structure data	6wsaC 2woxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5fhz-1 4dal-4 5izd-2 1wnd-d 6c43-1 4wp7-1 4qf6-1 4h73-6 5l13-2 6bpg-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-BupsA.00020.b

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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: NAD/NADP-dependent betaine aldehyde dehydrogenase

B: NAD/NADP-dependent betaine aldehyde dehydrogenase

hetero molecules

108 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NAD/NADP-dependent betaine aldehyde dehydrogenase

B: NAD/NADP-dependent betaine aldehyde dehydrogenase

hetero molecules

A: NAD/NADP-dependent betaine aldehyde dehydrogenase

B: NAD/NADP-dependent betaine aldehyde dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration
216 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.270, 156.700, 76.230
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-739- HOH
2	1	B-911- HOH

#1: Protein	NAD/NADP-dependent betaine aldehyde dehydrogenase / BADH Mass: 53132.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria) Strain: 1710b / Gene: betB, BURPS1710b_A0376 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JLL8, betaine-aldehyde dehydrogenase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1380 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.79 Å³/Da / Density % sol: 55.91 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: BupsA.00020.b.AE1.PS38619 at 34.72 mg/mL with 4 mM NAD against Morpheus condition H11: 10% PEG 4000, 20% glycerol, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL ...Details: BupsA.00020.b.AE1.PS38619 at 34.72 mg/mL with 4 mM NAD against Morpheus condition H11: 10% PEG 4000, 20% glycerol, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL lysine, 0.02 M DL serine, 0.1 M bicine/Trizma pH 8.5, unique puck ID qvy9-3, 314030h11

Crystal

Density Matthews: 2.79 Å³/Da / Density % sol: 55.91 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BupsA.00020.b.AE1.PS38619 at 34.72 mg/mL with 4 mM NAD against Morpheus condition H11: 10% PEG 4000, 20% glycerol, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 13, 2020

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.55→43.09 Å / Num. obs: 172302 / % possible obs: 99.9 % / Redundancy: 6.123 % / B_iso Wilson estimate: 20.398 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.076 / R_rim(I) all: 0.083 / Χ²: 1.051 / Net I/σ(I): 16.47 / Num. measured all: 1054995

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.55-1.59	6.003	0.566	3.02	75766	12626	12622	0.871	0.621	100
1.59-1.63	6.177	0.484	3.66	75896	12288	12287	0.896	0.529	100
1.63-1.68	6.192	0.407	4.4	74219	11986	11986	0.928	0.445	100
1.68-1.73	6.193	0.346	5.23	72269	11670	11670	0.946	0.378	100
1.73-1.79	6.2	0.279	6.52	69805	11259	11258	0.964	0.305	100
1.79-1.85	6.195	0.221	8.24	67795	10947	10944	0.977	0.241	100
1.85-1.92	6.179	0.18	10.15	65051	10531	10527	0.984	0.196	100
1.92-2	6.162	0.149	12.19	62880	10207	10204	0.989	0.163	100
2-2.09	6.134	0.119	15.01	59865	9765	9760	0.992	0.13	99.9
2.09-2.19	6.105	0.096	18.01	56859	9320	9313	0.994	0.106	99.9
2.19-2.31	6.098	0.086	19.71	54500	8941	8937	0.996	0.094	100
2.31-2.45	6.089	0.073	23.03	51206	8419	8409	0.997	0.079	99.9
2.45-2.62	6.087	0.064	25.44	48236	7935	7925	0.997	0.07	99.9
2.62-2.83	6.083	0.056	28.4	45096	7424	7413	0.998	0.062	99.9
2.83-3.1	6.098	0.047	32.64	41508	6815	6807	0.998	0.051	99.9
3.1-3.47	6.107	0.039	37.52	38072	6238	6234	0.999	0.042	99.9
3.47-4	6.101	0.034	41.74	33580	5504	5504	0.999	0.037	100
4-4.9	6.06	0.03	45.15	28383	4688	4684	0.999	0.033	99.9
4.9-6.93	5.992	0.031	42.62	22151	3697	3697	0.999	0.034	100
6.93-43.09	5.591	0.028	45.06	11858	2141	2121	0.999	0.031	99.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
PHENIX	1.17.1.3660	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2wox

2wox

Resolution: 1.55→43.09 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.56

	R_factor	Num. reflection	% reflection
R_free	0.1685	10050	6.05 %
R_work	0.1444	-	-
obs	0.1459	166209	96.41 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 75.66 Å² / B_iso mean: 17.3817 Å² / B_iso min: 6.48 Å²

Refinement step

Cycle: final / Resolution: 1.55→43.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7322	0	100	1388	8810
B_iso mean	-	-	31.67	30.65	-
Num. residues	-	-	-	-	978

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.55-1.57	0.2342	297	0.2064	4765	5062	89
1.57-1.59	0.2258	320	0.1963	4820	5140	90
1.59-1.61	0.2045	332	0.1904	4804	5136	91
1.61-1.63	0.2032	298	0.1848	4968	5266	92
1.63-1.65	0.1985	317	0.1795	4915	5232	92
1.65-1.67	0.2081	339	0.1728	4989	5328	93
1.67-1.69	0.1942	311	0.168	4989	5300	93
1.69-1.72	0.1738	301	0.1632	5041	5342	94
1.72-1.75	0.1864	338	0.168	5034	5372	94
1.75-1.77	0.209	330	0.1662	5131	5461	95
1.77-1.8	0.1992	310	0.163	5179	5489	96
1.8-1.84	0.1943	356	0.1552	5149	5505	96
1.84-1.87	0.1673	318	0.1523	5226	5544	97
1.87-1.91	0.1721	307	0.1533	5202	5509	97
1.91-1.95	0.1685	338	0.15	5223	5561	97
1.95-2	0.1776	323	0.1495	5196	5519	97
2-2.05	0.1743	361	0.148	5256	5617	98
2.05-2.1	0.182	318	0.1416	5303	5621	98
2.1-2.17	0.153	356	0.1412	5325	5681	99
2.17-2.24	0.1529	360	0.143	5301	5661	99
2.24-2.32	0.1757	372	0.1427	5296	5668	99
2.32-2.41	0.1655	332	0.1398	5334	5666	99
2.41-2.52	0.1724	306	0.1423	5388	5694	99
2.52-2.65	0.1658	351	0.1424	5364	5715	99
2.65-2.82	0.1684	363	0.1398	5379	5742	99
2.82-3.03	0.1653	356	0.1419	5417	5773	99
3.03-3.34	0.16	350	0.1326	5433	5783	99
3.34-3.82	0.1447	378	0.1263	5462	5840	100
3.82-4.81	0.1334	342	0.1127	5542	5884	100
4.81-43.09	0.1711	370	0.1458	5728	6098	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	0.8998	0.2739	-0.307	0.5673	-0.0922	0.4992	-0.0118	-0.0519	0.0039	0.0114	0.0104	0.0047	-0.0502	0.0228	-0.0002	0.1078	0.0013	-0.0058	0.0892	0.0093	0.0873	4.8953	21.6044	-2.128
2	2.8407	-1.8321	0.3214	1.9106	-0.5375	0.4007	-0.06	-0.1744	-0.1223	0.2156	0.0388	0.0804	-0.1477	-0.1008	0.0286	0.1821	-0.009	-0.0208	0.1904	0.0062	0.0936	16.6082	20.3711	11.9856
3	1.8134	-0.4014	0.2281	1.1019	-0.5439	0.8022	-0.0497	0.115	0.0329	0.0548	-0.2123	-0.4109	-0.1009	0.278	0.1681	0.0857	-0.0339	-0.0256	0.1765	0.0969	0.2299	36.0711	9.3761	4.6813
4	1.5165	0.5173	0.5957	1.0948	0.269	0.9822	0.0565	0.1515	0.1584	0.0323	-0.371	-0.5008	-0.2648	0.27	0.154	0.1732	-0.0845	-0.0533	0.1799	0.1248	0.2726	35.1443	22.8066	-6.3824
5	0.4825	0.1178	0.1904	0.1044	-0.0685	1.0768	-0.0539	-0.0107	0.0651	0.3443	-0.2424	-0.2891	-0.4957	0.3061	0.2143	0.2426	-0.1144	-0.1469	0.205	0.0948	0.2701	35.6294	18.1072	13.6004
6	0.8298	-0.2665	0.2528	1.0719	-0.722	1.184	-0.0722	-0.051	0.0427	0.171	-0.0328	-0.1206	-0.2074	0.0513	0.0897	0.1036	-0.0174	-0.0295	0.0755	0.0142	0.0952	21.8794	8.2056	13.5403
7	0.6326	-0.8068	-0.7885	1.0493	0.9811	1.2976	-0.0247	-0.1862	-0.0394	0.0599	-0.0027	-0.0047	0.0356	0.1756	0.0123	0.0785	0.0041	-0.0155	0.1137	0.0155	0.0687	-13.0517	11.9006	20.8831
8	4.1451	-0.9816	-0.8016	0.3516	0.3925	0.7038	-0.0129	-0.0917	0.1069	0.035	0.0371	-0.0076	-0.0499	0.0057	-0.0356	0.1063	-0.0116	-0.0205	0.0841	-0.0088	0.0665	4.1246	32.5675	47.2154
9	0.558	-0.2814	-0.1561	2.5844	0.1624	0.6139	-0.0267	-0.0274	-0.1202	-0.0133	0.0249	-0.2965	-0.0188	0.0691	0.0171	0.0701	-0.0006	-0.0326	0.1012	0.0005	0.0542	11.7176	12.4386	38.4262
10	0.3131	-0.4167	-0.1581	1.0385	0.392	0.4191	-0.0201	-0.0683	-0.0341	0.0492	0.0461	0.0209	-0.0059	-0.0103	0.0127	0.1033	0.0054	0.0008	0.1118	0.0103	0.1075	-7.2938	16.2394	41.6416
11	0.0293	-0.0188	-0.1505	0.3634	0.2911	0.5519	0.0094	0.0065	0.0011	-0.0095	-0.0152	-0.0215	-0.0145	-0.0061	-0.0101	0.096	0.0011	-0.0083	0.103	-0.0016	0.1018	6.9401	17.3331	30.4748
12	5.5193	1.0545	0.5482	0.4818	0.1656	0.376	-0.0833	0.2392	-0.2493	-0.0623	0.0628	-0.0827	-0.038	0.1715	0.0323	0.1322	0.0174	0.002	0.1826	-0.0095	0.0673	-6.026	25.8962	20.5487
13	1.8821	0.456	0.4511	1.3522	0.8864	2.4555	-0.0232	-0.0524	-0.0487	0.029	-0.0346	0.1296	-0.0154	-0.1256	0.0468	0.0638	0.0221	0.0013	0.0534	-0.0033	0.0759	-28.2237	24.4269	27.8816
14	0.955	-0.6417	0.7615	0.8048	-1.1569	2.9623	-0.1163	-0.1343	0.0788	0.1238	0.0125	-0.0621	-0.2291	-0.0293	0.093	0.1035	0.0124	-0.0098	0.0825	-0.0184	0.0755	-21.3932	36.1069	38.6712
15	0.6746	-0.0971	-0.1582	1.5494	1.0999	2.9517	0.0079	0.0554	0.0025	-0.106	-0.0477	0.0362	-0.1326	-0.0364	0.048	0.0859	0.021	-0.018	0.0704	0.0058	0.0704	-24.0372	31.7172	18.9273
16	1.2444	0.3787	0.3565	1.221	0.3504	0.9322	-0.0271	0.0476	-0.0266	-0.0502	-0.0023	0.0108	-0.0301	0.0225	0.0299	0.0689	0.0127	0.0039	0.0725	-0.0069	0.0654	-16.1089	16.9252	19.1451
17	0.4084	0.4315	-0.2908	0.9029	-0.7611	0.7828	-0.01	0.1304	0.0312	-0.0223	-0.0475	-0.0273	-0.0475	-0.1021	0.0175	0.0867	0.0009	-0.0259	0.1169	-0.0022	0.0778	15.9883	5.6346	12.7294
18	5.4186	0.1713	-1.244	0.4166	-0.3401	0.7766	0.009	0.1898	0.0411	-0.0235	0.019	-0.0295	-0.071	-0.0421	-0.0465	0.1157	0.0006	-0.0102	0.0857	0.0236	0.0665	10.6892	30.7757	-14.7471
19	1.4584	0.8931	-0.4198	1.7506	-0.2568	0.6066	-0.0204	0.0703	0.0261	0.0529	0.0148	0.247	-0.0396	-0.0953	0.0216	0.0825	0.0099	-0.0303	0.1017	0.0146	0.0423	-5.1474	15.8202	-5.7238
20	1.7609	0.5301	-1.5878	0.5935	-0.5073	1.596	-0.0791	0.0331	-0.0754	-0.0539	0.0045	-0.0527	0.0658	-0.0095	0.0709	0.0662	-0.0028	-0.0215	0.0736	-0.0004	0.0745	5.054	9.1849	0.2168

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 140 through 229 )	B	140 - 229
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 230 through 265 )	B	230 - 265
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 266 through 311 )	B	266 - 311
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 312 through 370 )	B	312 - 370
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 371 through 408 )	B	371 - 408
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 409 through 464 )	B	409 - 464
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 465 through 490 )	B	465 - 490
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 2 through 42 )	A	2 - 42
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 43 through 81 )	A	43 - 81
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 82 through 122 )	A	82 - 122
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 123 through 229 )	A	123 - 229
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 230 through 265 )	A	230 - 265
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 266 through 311 )	A	266 - 311
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 312 through 370 )	A	312 - 370
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 371 through 408 )	A	371 - 408
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 409 through 464 )	A	409 - 464
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 465 through 490 )	A	465 - 490
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 2 through 42 )	B	2 - 42
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 43 through 81 )	B	43 - 81
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 82 through 139 )	B	82 - 139

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

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