PDB-4cbb: APO FORM OF BETAINE ALDEHYDE DEHYDROGENASE FROM Pseudomonas aeruginosa

ID or keywords:

Entry

Database: PDB / ID: 4cbb

Title

APO FORM OF BETAINE ALDEHYDE DEHYDROGENASE FROM Pseudomonas aeruginosa

Components

BETAINE ALDEHYDE DEHYDROGENASE

Keywords

OXIDOREDUCTASE / ALDEHYDE OXIDATION

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

PSEUDOMONAS AERUGINOSA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Gonzalez-Segura, L. / Diaz-Sanchez, A.G. / Munoz-Clares, R.A.

Citation

Journal: To be Published
Title: The Structural Bases of the Dual Coenzyme Specificity of Betaine Aldehyde Dehydrogenase from Pseudomonas Aeruginosa
Authors: Diaz-Sanchez, A.G. / Gonzalez-Segura, L. / Rodriguez-Sotres, R. / Mujica-Jimenez, C. / Munoz-Clares, R.A.

History

Deposition	Oct 11, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 29, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4cbb.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb4cbb.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	4cbb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4cbb_validation.pdf.gz	3.3 MB	Display	wwPDB validaton report
Full document	4cbb_full_validation.pdf.gz	3.3 MB	Display
Data in XML	4cbb_validation.xml.gz	170.6 KB	Display
Data in CIF	4cbb_validation.cif.gz	251 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cb/4cbb ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cbb	HTTPS FTP

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Related structure data

Related structure data	4cazC 2wmeS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6bpg-1 3zqa-d 2xdr-d 5gtl-d 4caz-1 6bpg-2 2wme-1 5gtk-d 3ek1-1 4qje-d Search similar-shape structures by Omokage search (details) 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (8) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (8) #92 - Aug 2007 Anabolic Steroids similarity (1) #174 - Jun 2014 GFP-like Proteins similarity (1)

Deposited unit

A: BETAINE ALDEHYDE DEHYDROGENASE

B: BETAINE ALDEHYDE DEHYDROGENASE

C: BETAINE ALDEHYDE DEHYDROGENASE

D: BETAINE ALDEHYDE DEHYDROGENASE

E: BETAINE ALDEHYDE DEHYDROGENASE

F: BETAINE ALDEHYDE DEHYDROGENASE

G: BETAINE ALDEHYDE DEHYDROGENASE

H: BETAINE ALDEHYDE DEHYDROGENASE

hetero molecules

434 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

E: BETAINE ALDEHYDE DEHYDROGENASE

F: BETAINE ALDEHYDE DEHYDROGENASE

G: BETAINE ALDEHYDE DEHYDROGENASE

H: BETAINE ALDEHYDE DEHYDROGENASE

hetero molecules

defined by author&software
217 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: BETAINE ALDEHYDE DEHYDROGENASE

B: BETAINE ALDEHYDE DEHYDROGENASE

C: BETAINE ALDEHYDE DEHYDROGENASE

D: BETAINE ALDEHYDE DEHYDROGENASE

hetero molecules

defined by author&software
217 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	332.320, 131.339, 100.815
Angle α, β, γ (deg.)	90.00, 95.02, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	BETAINE ALDEHYDE DEHYDROGENASE / BADH Mass: 53259.066 Da / Num. of mol.: 8 / Fragment: RESIDUES 2-490 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PCALBETB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HTJ1, betaine-aldehyde dehydrogenase

#1: Protein

BETAINE ALDEHYDE DEHYDROGENASE / BADH

Mass: 53259.066 Da / Num. of mol.: 8 / Fragment: RESIDUES 2-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PCALBETB / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HTJ1, betaine-aldehyde dehydrogenase

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Non-polymers , 6 types, 3715 molecules

#2: Chemical	ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL Mass: 154.251 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 Mass: 354.436 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₈ / Comment: precipitant*YM
#5: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	... ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3643 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	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: 2.49 Å³/Da / Density % sol: 50.61 % / Description: NONE
Crystal grow	pH: 7.5 Details: CRYSTALS WERE GROWN IN 85 MM HEPES PH 7.5, 8.5% (V:V) ISOPROPANOL, 17% (W:V)PEG 4000, 15% (V:V) GLYCEROL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9795
Detector	Type: MARRESEARCH / Detector: CCD / Date: Nov 9, 2008 / Details: VERTICAL FOCUSING
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.8→20 Å / Num. obs: 392152 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / B_iso Wilson estimate: 17.22 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 7.9
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.03 / Mean I/σ(I) obs: 2.9 / % possible all: 95.4

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WME

2wme

Resolution: 1.8→29.824 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 16.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1827	19716	5 %
R_work	0.147	-	-
obs	0.1488	392133	98.65 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 24 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.824 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	29952	0	452	3643	34047

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	31562
X-RAY DIFFRACTION	f_angle_d	1.066	42761
X-RAY DIFFRACTION	f_dihedral_angle_d	13.529	11819
X-RAY DIFFRACTION	f_chiral_restr	0.071	4793
X-RAY DIFFRACTION	f_plane_restr	0.004	5620

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 (%)
1.8-1.8205	0.2551	595	0.218	10925	X-RAY DIFFRACTION	87
1.8205-1.8419	0.2323	657	0.1923	12473	X-RAY DIFFRACTION	100
1.8419-1.8643	0.2282	712	0.1864	12462	X-RAY DIFFRACTION	100
1.8643-1.8879	0.2365	618	0.1802	12461	X-RAY DIFFRACTION	100
1.8879-1.9128	0.2193	657	0.1734	12528	X-RAY DIFFRACTION	100
1.9128-1.939	0.2198	679	0.177	12543	X-RAY DIFFRACTION	100
1.939-1.9667	0.2083	622	0.1692	12519	X-RAY DIFFRACTION	100
1.9667-1.996	0.1922	667	0.162	12507	X-RAY DIFFRACTION	100
1.996-2.0272	0.2065	649	0.1553	12510	X-RAY DIFFRACTION	100
2.0272-2.0604	0.1955	640	0.1534	12532	X-RAY DIFFRACTION	100
2.0604-2.0959	0.1932	629	0.1455	12552	X-RAY DIFFRACTION	100
2.0959-2.134	0.1888	655	0.1436	12476	X-RAY DIFFRACTION	100
2.134-2.1751	0.1769	687	0.1453	12496	X-RAY DIFFRACTION	100
2.1751-2.2195	0.1784	683	0.1435	12467	X-RAY DIFFRACTION	100
2.2195-2.2677	0.1916	668	0.1467	12576	X-RAY DIFFRACTION	100
2.2677-2.3204	0.1781	681	0.1397	12462	X-RAY DIFFRACTION	100
2.3204-2.3784	0.1765	654	0.14	12566	X-RAY DIFFRACTION	100
2.3784-2.4427	0.1897	644	0.1438	12557	X-RAY DIFFRACTION	100
2.4427-2.5146	0.1983	661	0.1444	12473	X-RAY DIFFRACTION	99
2.5146-2.5957	0.1911	671	0.1438	12502	X-RAY DIFFRACTION	99
2.5957-2.6884	0.1831	636	0.1422	12541	X-RAY DIFFRACTION	99
2.6884-2.796	0.1779	635	0.1414	12563	X-RAY DIFFRACTION	99
2.796-2.9231	0.1717	663	0.1424	12464	X-RAY DIFFRACTION	99
2.9231-3.0771	0.1834	699	0.1431	12463	X-RAY DIFFRACTION	99
3.0771-3.2696	0.1798	698	0.1443	12413	X-RAY DIFFRACTION	99
3.2696-3.5217	0.1766	646	0.1388	12486	X-RAY DIFFRACTION	99
3.5217-3.8754	0.1544	664	0.1326	12452	X-RAY DIFFRACTION	98
3.8754-4.4346	0.1637	655	0.1298	12410	X-RAY DIFFRACTION	98
4.4346-5.5812	0.1576	636	0.1391	11783	X-RAY DIFFRACTION	93
5.5812-29.8285	0.1781	655	0.161	12255	X-RAY DIFFRACTION	96

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	0.2451	0.0321	0.0948	0.3371	-0.0791	0.3431	-0.0097	-0.0381	-0.0024	0.0797	-0.0067	-0.0139	-0.0372	-0.0118	-0.0076	0.1096	-0.0004	0.0032	0.1076	0.008	0.072	43.83	1.1663	38.3503
2	0.2532	0.0106	0.0784	0.4168	-0.1066	0.3612	0.015	-0.0294	-0.0667	-0.0526	0.0233	0.0807	0.0803	-0.0882	0.0048	0.1138	-0.0274	-0.0084	0.1204	0.0207	0.1101	27.5861	-22.876	18.2058
3	0.3158	0.041	-0.0031	0.3912	-0.0908	0.673	-0.0429	0.1083	0.0093	-0.1633	0.0077	-0.0924	0.0215	0.1792	-0.0422	0.1593	-0.0166	0.0499	0.1858	0.0223	0.0977	57.8354	-0.1916	-8.97
4	0.2238	-0.0012	0.043	0.408	-0.1587	0.5108	-0.0394	0.0646	0.0895	-0.0715	0.0456	0.0777	-0.1242	-0.0899	0.0281	0.1648	0.0062	-0.0213	0.141	0.0392	0.1257	31.172	22.1361	-1.074
5	0.3328	0.3491	-0.0826	0.8315	-0.0019	0.1297	0.0699	-0.0499	-0.0742	0.1836	-0.0562	-0.0942	0.029	0.0071	0.0044	0.1415	0.0012	-0.0169	0.1035	0.031	0.1235	45.5946	39.4841	63.9598
6	0.3143	0.1637	-0.0001	0.8701	0.0422	0.3969	-0.0147	0.0771	0.0205	-0.1525	0.0058	0.2216	0.0265	-0.0768	0.0286	0.1138	0.0041	-0.0154	0.1239	0.0195	0.1769	29.919	55.8815	36.2072
7	0.4094	0.0105	0.0681	0.6615	0.0411	0.2271	0.002	-0.0215	0.0889	0.1238	-0.009	0.0079	-0.0364	0.0114	0.0151	0.1239	-0.0061	0.0136	0.1081	0.019	0.1575	51.0746	88.3456	61.7485
8	0.3555	0.1411	0.0445	0.6896	0.1474	0.4722	0.0515	-0.1387	0.1723	0.3184	-0.1163	0.3186	-0.0224	-0.1632	0.0147	0.2682	-0.0213	0.1565	0.1754	-0.0561	0.2959	23.5192	76.551	80.5032
9	0.0973	0.1074	0.0162	0.3037	0.105	0.037	-0.0292	0.0397	-0.0152	-0.0194	-0.012	0.0707	-0.0237	0.0668	-0.0006	0.2849	0.0089	-0.0553	0.3639	0.0767	0.2614	43.9558	22.9192	24.8143
10	0.0437	0.0955	0.0496	0.3303	0.0853	0.0748	0.0179	-0.0018	0.0251	0.0351	-0.0324	0.0707	0.0145	-0.0262	0.0161	0.1847	-0.0012	0.0245	0.2328	0.0385	0.2234	38.8073	32.5767	36.0688
11	0.0461	0.0441	0.013	0.2923	0.0762	0.0674	0.0002	0.0107	0.0311	0.0121	-0.0091	0.0363	-0.002	-0.0073	0.0083	0.137	-0.0009	-0.0032	0.1937	0.037	0.1624	39.9989	30.9705	35.4891
12	0.0803	0.1126	0.0169	0.3213	0.1418	0.1254	0.0484	0.0148	0.0487	0.0086	0.0345	0.0582	0.0109	-0.0313	0.0207	0.2466	-0.0237	0.0443	0.3929	0.079	0.3062	46.0928	23.9835	32.4336
13	0.0943	0.0454	0.0728	0.3576	0.031	0.1277	0.0009	0.0305	0.0968	-0.0232	-0.0801	0.0891	-0.0078	0	0.0159	0.453	-0.0559	0.0597	0.5265	0.0415	0.5245	38.6074	32.6169	35.9066

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A
2	X-RAY DIFFRACTION	2	CHAIN B
3	X-RAY DIFFRACTION	3	CHAIN C
4	X-RAY DIFFRACTION	4	CHAIN D
5	X-RAY DIFFRACTION	5	CHAIN E
6	X-RAY DIFFRACTION	6	CHAIN F
7	X-RAY DIFFRACTION	7	CHAIN G
8	X-RAY DIFFRACTION	8	CHAIN H
9	X-RAY DIFFRACTION	9	CHAIN Q
10	X-RAY DIFFRACTION	10	CHAIN R
11	X-RAY DIFFRACTION	11	CHAIN S
12	X-RAY DIFFRACTION	12	CHAIN I
13	X-RAY DIFFRACTION	13	CHAIN L

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Protein , 1 types, 8 molecules ABCDEFGH

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Non-polymers , 6 types, 3715 molecules

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