PDB-5j6b: Crystal structure of Aldehyde dehydrogenase from Burkholderia tha...

ID or keywords:

Entry

Database: PDB / ID: 5j6b

Title

Crystal structure of Aldehyde dehydrogenase from Burkholderia thailandensis in covelent complex with NADPH

Components

Aldehyde dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / ALDEHYDE DEHYDROGENASE / NADP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

lactaldehyde dehydrogenase (NAD+) activity / nucleotide binding
Similarity search - Function

Biological species

Burkholderia thailandensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To Be Published
Title: Crystal structure of Aldehyde dehydrogenase from Burkholderia thailandensis in covelent complex with NADPH
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Apr 4, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5j6b.cif.gz	753.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5j6b.ent.gz	623.5 KB	Display	PDB format
PDBx/mmJSON format	5j6b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5j6b_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	5j6b_full_validation.pdf.gz	1.7 MB	Display
Data in XML	5j6b_validation.xml.gz	78.5 KB	Display
Data in CIF	5j6b_validation.cif.gz	115.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j6/5j6b ftp://data.pdbj.org/pub/pdb/validation_reports/j6/5j6b	HTTPS FTP

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Related structure data

Related structure data	3pqaS S: Starting model for refinement
Similar structure data	5kf0-d 5jry-1 5f2c-2 3jz4-d 5eeb-2 5n5s-1 3k2w-2 4v6h-6 3inj-1 5abm-1 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: ButhA.00020.t

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (5) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (5) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Aldehyde dehydrogenase

B: Aldehyde dehydrogenase

C: Aldehyde dehydrogenase

D: Aldehyde dehydrogenase

hetero molecules

214 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	83.520, 143.660, 167.430
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Aldehyde dehydrogenase / Aldehyde dehydrogenase family protein Mass: 52788.211 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301) (bacteria) Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_II0498, DR63_5272 / Plasmid: ButhA.00020.t.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T801
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1431 / Source method: isolated from a natural source / Formula: H₂O
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: 2.38 Å³/Da / Density % sol: 48 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: RigakuReagents JCSG+ screen H5: 45% MPD, 200mM Ammonium acetate, 100mM BisTris/HCl pH 5.5; ButhA.00020.t.B1.PW37792 at 22.7 mg/ml + 3mM NADP; cryo: direct; tray: 26729h5, puck sja1-10 PH range: 5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 17, 2015
Radiation	Monochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. obs: 146312 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / B_iso Wilson estimate: 27.86 Å² / R_merge(I) obs: 0.093 / Net I/σ(I): 14.3
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.513 / Mean I/σ(I) obs: 3.55 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
ARP		model building
Coot		model building
PHENIX	(DEV_2356: ???)	refinement
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3pqa

3pqa

Resolution: 1.95→46.4 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 17.87

	R_factor	Num. reflection	% reflection
R_free	0.187	2012	1.38 %
R_work	0.149	-	-
obs	0.149	146283	99.5 %

Solvent computation

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

Displacement parameters

B_iso mean: 25.19 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→46.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14416	0	196	1431	16043

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	15091
X-RAY DIFFRACTION	f_angle_d	0.85	20543
X-RAY DIFFRACTION	f_dihedral_angle_d	13.297	9177
X-RAY DIFFRACTION	f_chiral_restr	0.051	2305
X-RAY DIFFRACTION	f_plane_restr	0.005	2769

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	0.814	-0.1072	-0.2018	0.5909	0.0612	1.2954	-0.0091	0.0136	0.27	-0.0236	0.0271	0.2237	-0.2711	-0.0458	-0.0198	0.1899	0.0185	0.0132	0.118	0.0418	0.3009	85.45	177.4493	31.468
2	0.4138	0.0666	-0.254	1.1639	0.5272	0.4195	-0.0135	0.0381	0.0568	0.0003	0.0632	0.1218	0.0046	0.0199	-0.0687	0.1599	0.0085	-0.0117	0.1519	0.0386	0.1476	94.8761	159.508	25.2185
3	0.4041	-0.1026	0.2314	0.6583	-0.2276	0.7963	-0.0071	0.0251	0.0724	0.0377	-0.0069	0.2447	-0.0497	-0.0961	0.0181	0.1331	0.0177	0.0325	0.1338	0.0345	0.23	81.9422	163.6046	32.3024
4	2.3418	-0.3134	0.2089	1.4359	0.3624	0.3046	-0.013	-0.0655	0.1851	0.2013	0.0476	0.1688	-0.1568	-0.0015	0.0083	0.238	0.0052	0.0823	0.1422	-0.0048	0.1624	97.2293	160.7566	54.4704
5	0.6927	0.0924	-0.0219	1.0087	0.1595	0.5835	-0.0623	-0.1466	0.0192	0.3321	0.0304	0.2794	0.0696	-0.0781	0.0189	0.2389	0.0235	0.0983	0.1525	0.022	0.1699	90.7741	155.2649	56.2546
6	0.3462	0.4474	0.3122	0.5801	0.4731	1.5796	-0.0711	0.0482	0.0274	-0.0618	0.0216	0.1195	-0.1533	0.0831	0.0111	0.1379	0.0113	0.0073	0.1396	0.0445	0.1858	92.5578	151.4004	23.0683
7	1.1668	0.5467	-0.1409	0.678	-0.2168	0.7859	-0.0832	0.0927	-0.1333	-0.0647	0.0562	0.06	0.156	-0.0731	0.0095	0.1449	-0.0267	0.032	0.1193	0.0007	0.1741	81.2944	121.1467	23.1176
8	1.0708	0.6622	0.3688	1.0805	0.5681	0.4501	-0.0439	0.1122	-0.0401	-0.071	0.0867	0.0248	-0.0523	0.0529	-0.0677	0.1495	-0.0355	0.0147	0.1595	0.0309	0.1195	93.606	137.9357	24.1513
9	0.9539	0.6199	-0.0567	0.8393	-0.3467	0.5796	-0.0634	0.125	0.119	-0.0464	0.0498	0.2058	0.0057	-0.0896	-0.0363	0.1131	-0.0252	-0.0017	0.1367	0.0137	0.1708	78.7358	134.7544	22.5235
10	0.3825	-0.4721	0.2024	0.9521	0.0864	0.4111	-0.1188	0.4359	-0.1109	-0.2667	0.2257	0.1208	0.1792	-0.0134	-0.1385	0.2966	-0.1747	-0.0687	0.4499	0.02	0.1514	84.1522	136.7074	-3.4766
11	1.0934	0.2177	-0.4258	0.3305	0.0639	0.7001	-0.2507	0.5679	0.3028	-0.2879	0.2651	0.2938	0.0081	-0.3045	0.0538	0.2541	-0.15	-0.1453	0.4554	0.1619	0.2578	78.1143	143.1578	-2.8099
12	0.5633	0.3193	0.5764	0.6607	0.7059	2.003	-0.0629	0.1075	0.16	-0.0126	0.0209	0.1571	0.0745	0.0434	0.0247	0.1187	-0.0253	0.013	0.1113	0.0368	0.1626	93.0765	145.9482	26.714
13	0.8911	-0.2994	0.8325	1.1093	-1.1716	2.9273	0.0419	0.2181	-0.2932	-0.305	-0.0076	-0.1386	0.5218	0.2988	-0.0258	0.2967	0.0532	0.0597	0.222	-0.0752	0.2662	131.0513	119.5896	9.4895
14	3.2965	-1.7892	2.6974	2.0143	-1.7842	3.1759	0.2329	0.0446	-0.6004	-0.2111	0.1122	0.1959	0.5513	-0.0778	-0.3166	0.2277	-0.0324	-0.003	0.1513	-0.0038	0.3031	115.7632	119.6888	17.2043
15	1.1574	-0.5472	0.2085	1.1533	-0.0393	0.2751	-0.0075	-0.0168	-0.1205	0.009	0.0809	0.08	-0.012	-0.0248	-0.0946	0.1227	-0.0121	0.022	0.139	0.021	0.1137	115.1208	137.2456	17.1917
16	0.396	-0.086	0.0655	0.5596	0.1464	1.539	0.0054	0.0499	-0.1022	-0.1033	-0.0002	-0.0896	0.0671	0.1494	-0.0194	0.1328	0.0033	0.0329	0.1872	-0.004	0.1728	129.2562	131.5895	17.3813
17	3.7574	-0.9443	-1.7816	3.1382	1.007	2.6177	-0.1715	-0.1776	-0.4416	0.1571	0.0138	0.1046	0.4172	0.1247	0.1383	0.1238	0.0285	-0.0104	0.1717	0.0698	0.1933	123.4211	126.2586	43.1885
18	1.3833	-0.247	-0.1077	1.5808	0.102	1.2367	-0.0767	-0.2417	-0.204	0.1623	0.0981	-0.1804	0.1615	0.2287	-0.0062	0.1336	0.0369	-0.0182	0.2342	0.0483	0.1842	134.5074	127.6778	45.2568
19	2.2222	0.1847	-0.1115	1.1326	0.3417	1.5687	-0.0215	-0.0805	0.058	0.1282	0.0286	0.0122	-0.122	0.0595	-0.0079	0.13	0.0174	0.0168	0.126	0.0198	0.108	120.926	140.6029	40.4063
20	0.195	-0.1048	0.4471	1.5217	-1.3705	2.2974	-0.0176	0.0083	0.0186	-0.1189	0.0887	0.0706	0.0504	0.0226	-0.1089	0.118	-0.015	0.0206	0.129	0.0128	0.1466	116.9461	145.6091	17.1127
21	0.7855	0.1992	-0.2837	1.498	-1.9397	4.0097	0.0196	0.0529	0.2419	0.0834	-0.0009	-0.1422	-0.4115	0.2062	0.0216	0.2651	-0.1223	0.0307	0.2229	0.0037	0.2745	137.4448	179.6721	19.0125
22	1.2923	0.3379	-0.4938	0.5355	-0.149	1.4218	0.04	-0.0612	0.178	0.0237	0.0868	-0.0019	-0.2616	0.0114	-0.0956	0.2004	-0.0585	0.0423	0.109	-0.029	0.1507	123.8614	171.2848	25.495
23	0.4019	-0.0279	-0.3528	1.1216	-0.247	0.5621	0.0436	0.0714	0.0476	-0.0685	0.068	0.1359	-0.0783	-0.011	-0.131	0.1411	-0.0433	-0.0093	0.1589	0.0319	0.1217	117.3212	158.0444	22.9638
24	0.5761	0.0716	0.2047	0.5337	-0.0185	0.7955	-0.0017	0.0324	0.0358	-0.0696	0.0137	-0.1064	-0.1013	0.1958	0.0012	0.1569	-0.0507	0.0451	0.1652	0.0247	0.1528	130.7153	162.3733	17.1323
25	2.1058	0.4471	1.1126	0.4167	0.6453	1.9422	-0.0892	-0.0372	0.214	-0.1897	0.0818	0.0571	-0.2371	0.0381	0.0705	0.2823	-0.0466	0.0203	0.1659	0.0588	0.1612	115.7254	168.2828	-4.8283
26	0.9109	0.0069	0.3783	1.4058	-0.2779	1.4798	0.001	0.2191	0.097	-0.3283	0.012	-0.1351	-0.0708	0.2249	-0.0081	0.292	-0.0464	0.0545	0.2262	0.0315	0.1297	124.6881	166.4945	-10.8064
27	1.8528	-0.048	0.1134	0.7362	-0.3844	1.3192	0.0005	0.0581	-0.1411	-0.2155	0.091	0.0786	0.1647	-0.0738	-0.0911	0.2152	-0.0543	-0.0058	0.1533	0.0403	0.1276	112.7725	154.6536	-0.6724
28	0.4208	-0.4041	0.0926	0.4882	-0.4961	1.3493	-0.0324	-0.0157	-0.0728	0.0244	0.0549	0.0506	-0	-0.0236	-0.0568	0.1319	-0.034	0.0236	0.1273	0.0179	0.1428	118.2257	149.5539	22.4285

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