PDB-2opx: Crystal Structure of Lactaldehyde Dehydrogenase from Escherichia coli

ID or keywords:

Entry

Database: PDB / ID: 2opx

Title

Crystal Structure of Lactaldehyde Dehydrogenase from Escherichia coli

Components

Aldehyde dehydrogenase A

Keywords

OXIDOREDUCTASE / Rossmann fold / Dehydrogenase / deoxycholate / Protein detergent complex

Function / homology

Function and homology information

glycolaldehyde dehydrogenase / glycolaldehyde dehydrogenase (NAD+) activity / lactaldehyde dehydrogenase / succinate-semialdehyde dehydrogenase (NAD+) activity / lactaldehyde dehydrogenase (NAD+) activity / gamma-aminobutyric acid catabolic process / L-fucose catabolic process / rhamnose catabolic process / protein-containing complex / identical protein binding / cytosol
Similarity search - Function

Biological species

Escherichia coli BL21 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.53 Å

Authors

Francuski, D. / Rossocha, M. / Saenger, W.

Citation

Journal: To be Published
Title: Crystal Structure of Lactaldehyde Dehydrogenase from Escherichia coli
Authors: Francuski, D. / Rossocha, M. / Saenger, W.

History

Deposition	Jan 30, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 20, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2opx.cif.gz	114.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2opx.ent.gz	85.2 KB	Display	PDB format
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Others	Other downloads

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Validation report

Summary document	2opx_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	2opx_full_validation.pdf.gz	1.2 MB	Display
Data in XML	2opx_validation.xml.gz	24.1 KB	Display
Data in CIF	2opx_validation.cif.gz	34.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/op/2opx ftp://data.pdbj.org/pub/pdb/validation_reports/op/2opx	HTTPS FTP

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Related structure data

Similar structure data	2ilu-1 2hg2-1 1wnb-d 2w8n-1 4ywe-2 3n80-2 4npi-d 3n82-2 5abm-1 5x5u-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

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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: Aldehyde dehydrogenase A

hetero molecules

53.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aldehyde dehydrogenase A

hetero molecules

A: Aldehyde dehydrogenase A

hetero molecules

A: Aldehyde dehydrogenase A

hetero molecules

A: Aldehyde dehydrogenase A

hetero molecules

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

Unit cell

Length a, b, c (Å)	141.811, 141.811, 107.861
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	181
Space group name H-M	P6₄22

#1: Protein	Aldehyde dehydrogenase A / E.C.1.2.1.22 / Lactaldehyde dehydrogenase Mass: 52318.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Species: Escherichia coli / Strain: BL21 (DE3) / References: UniProt: P25553, lactaldehyde dehydrogenase
#2: Chemical	ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID Mass: 392.572 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₄H₄₀O₄ / Comment: detergent*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.87 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.4M Na-citrate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1
1,2		1

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 1 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 16, 2006 / Details: mirrors

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si-111 crystal	SINGLE WAVELENGTH	M	x-ray	1
2	Si-111 crystal	MAD	M	x-ray	1

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

R_sym value: 0.162 / D res low: 50 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	D res high (Å)	Num. obs	% possible obs
20.3	1	5.7	506056	0.137	0.88	2.42	24955	97
21.6	2	5.5	549527	0.143	0.79	2.42	25416	98.7
13.2	3	5	428038	0.154	0.8	2.23	32372	98.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Chi squared	Redundancy
5.21	50	100	1	0.065	0.046	1.185	23.3
4.14	5.21	100	1	0.069	0.079	0.984	24.8
3.61	4.14	100	1	0.095	0.077	0.887	25
3.28	3.61	100	1	0.142	0.079	0.8	25.2
3.05	3.28	100	1	0.221	0.102	0.752	25.4
2.87	3.05	100	1	0.334	0.141	0.753	24.3
2.73	2.87	100	1	0.461	0.21	0.804	20.4
2.61	2.73	99.4	1	0.564	0.31	0.855	14.3
2.51	2.61	96.6	1	0.619	0.416	0.854	9.5
2.42	2.51	73.5	1	0.537	0.515	0.985	5.5
5.21	50	100	2	0.053	0.046	0.942	21
4.14	5.21	100	2	0.058	0.079	0.875	22.4
3.61	4.14	100	2	0.081	0.077	0.828	22.6
3.28	3.61	100	2	0.122	0.079	0.78	22.8
3.05	3.28	100	2	0.189	0.102	0.74	23
2.87	3.05	100	2	0.288	0.141	0.711	22.6
2.73	2.87	100	2	0.415	0.21	0.705	22.6
2.61	2.73	100	2	0.553	0.31	0.727	22.1
2.51	2.61	100	2	0.679	0.416	0.705	21
2.42	2.51	87	2	0.579	0.515	0.914	15.3
4.8	50	100	3	0.054	0.046	1.106	13.5
3.81	4.8	100	3	0.06	0.079	0.913	14.3
3.33	3.81	100	3	0.101	0.077	0.836	14.4
3.03	3.33	100	3	0.169	0.079	0.755	14.5
2.81	3.03	100	3	0.286	0.102	0.705	14.5
2.64	2.81	100	3	0.421	0.141	0.697	14.1
2.51	2.64	100	3	0.533	0.21	0.707	13.7
2.4	2.51	100	3	0.701	0.31	0.704	13
2.31	2.4	99.9	3	0.844	0.416	0.674	11.5
2.23	2.31	87.9	3	0.695	0.515	0.931	7.9

Reflection

Resolution: 2.53→123.091 Å / Num. all: 25078 / Num. obs: 21449 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 14.4 % / B_iso Wilson estimate: 20.8 Å² / R_merge(I) obs: 0.162 / R_sym value: 0.162 / Net I/σ(I): 4.6

Reflection shell

Resolution: 2.53→2.67 Å / Redundancy: 14.4 % / R_merge(I) obs: 0.515 / Mean I/σ(I) obs: 1.5 / Num. measured all: 44323 / Num. unique all: 3079 / R_sym value: 0.515 / % possible all: 99.3

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Phasing

Phasing

Method:

MAD

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	2.23	49.92	21419	3506
ISO_2	0.544	0.709	2.23	49.92	21407	3505
ISO_3	0.706	0.837	2.23	49.92	21414	3505
ANO_1	0.952	0	2.23	49.92	20535	0
ANO_2	0.973	0	2.23	49.92	21765	0
ANO_3	0.978	0	2.23	49.92	27894	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Reflection acentric	Reflection centric
ISO_1	9.79-49.92	0	0	259	210
ISO_1	6.99-9.79	0	0	527	211
ISO_1	5.73-6.99	0	0	701	211
ISO_1	4.97-5.73	0	0	854	214
ISO_1	4.45-4.97	0	0	982	214
ISO_1	4.06-4.45	0	0	1085	215
ISO_1	3.76-4.06	0	0	1195	201
ISO_1	3.52-3.76	0	0	1291	222
ISO_1	3.32-3.52	0	0	1386	216
ISO_1	3.15-3.32	0	0	1465	210
ISO_1	3.01-3.15	0	0	1546	215
ISO_1	2.88-3.01	0	0	1629	213
ISO_1	2.77-2.88	0	0	1687	210
ISO_1	2.67-2.77	0	0	1768	211
ISO_1	2.58-2.67	0	0	1813	214
ISO_1	2.49-2.58	0	0	1832	196
ISO_1	2.42-2.49	0	0	1399	123
ISO_1	2.35-2.42	0	0	0	0
ISO_1	2.29-2.35	0	0	0	0
ISO_1	2.23-2.29	0	0	0	0
ANO_1	9.79-49.92	0.255	0	259	0
ANO_1	6.99-9.79	0.388	0	527	0
ANO_1	5.73-6.99	0.547	0	701	0
ANO_1	4.97-5.73	0.623	0	854	0
ANO_1	4.45-4.97	0.68	0	982	0
ANO_1	4.06-4.45	0.759	0	1085	0
ANO_1	3.76-4.06	0.831	0	1195	0
ANO_1	3.52-3.76	0.872	0	1291	0
ANO_1	3.32-3.52	0.927	0	1386	0
ANO_1	3.15-3.32	0.958	0	1465	0
ANO_1	3.01-3.15	0.977	0	1546	0
ANO_1	2.88-3.01	0.985	0	1629	0
ANO_1	2.77-2.88	0.99	0	1687	0
ANO_1	2.67-2.77	0.994	0	1748	0
ANO_1	2.58-2.67	0.997	0	1710	0
ANO_1	2.49-2.58	0.999	0	1530	0
ANO_1	2.42-2.49	0.998	0	940	0
ANO_1	2.35-2.42	0	0	0	0
ANO_1	2.29-2.35	0	0	0	0
ANO_1	2.23-2.29	0	0	0	0
ISO_2	9.79-49.92	0.63	0.636	259	210
ISO_2	6.99-9.79	0.606	0.86	527	211
ISO_2	5.73-6.99	0.662	0.803	701	211
ISO_2	4.97-5.73	0.636	0.767	854	214
ISO_2	4.45-4.97	0.659	0.755	982	214
ISO_2	4.06-4.45	0.647	0.753	1085	215
ISO_2	3.76-4.06	0.693	0.758	1195	201
ISO_2	3.52-3.76	0.7	0.768	1291	222
ISO_2	3.32-3.52	0.726	0.745	1386	216
ISO_2	3.15-3.32	0.731	0.853	1465	210
ISO_2	3.01-3.15	0.765	0.794	1546	215
ISO_2	2.88-3.01	0.724	0.878	1629	213
ISO_2	2.77-2.88	0.614	0.773	1687	210
ISO_2	2.67-2.77	0.502	0.698	1768	211
ISO_2	2.58-2.67	0.387	0.537	1813	214
ISO_2	2.49-2.58	0.406	0.508	1832	196
ISO_2	2.42-2.49	0.573	0.69	1387	122
ISO_2	2.35-2.42	0	0	0	0
ISO_2	2.29-2.35	0	0	0	0
ISO_2	2.23-2.29	0	0	0	0
ANO_2	9.79-49.92	0.317	0	259	0
ANO_2	6.99-9.79	0.496	0	527	0
ANO_2	5.73-6.99	0.719	0	701	0
ANO_2	4.97-5.73	0.768	0	854	0
ANO_2	4.45-4.97	0.773	0	982	0
ANO_2	4.06-4.45	0.867	0	1085	0
ANO_2	3.76-4.06	0.9	0	1195	0
ANO_2	3.52-3.76	0.923	0	1291	0
ANO_2	3.32-3.52	0.963	0	1386	0
ANO_2	3.15-3.32	0.978	0	1465	0
ANO_2	3.01-3.15	0.984	0	1546	0
ANO_2	2.88-3.01	0.994	0	1629	0
ANO_2	2.77-2.88	0.996	0	1687	0
ANO_2	2.67-2.77	0.997	0	1768	0
ANO_2	2.58-2.67	0.997	0	1837	0
ANO_2	2.49-2.58	0.999	0	1900	0
ANO_2	2.42-2.49	0.998	0	1653	0
ANO_2	2.35-2.42	0	0	0	0
ANO_2	2.29-2.35	0	0	0	0
ANO_2	2.23-2.29	0	0	0	0
ISO_3	9.79-49.92	0.574	0.584	259	209
ISO_3	6.99-9.79	0.609	0.646	527	211
ISO_3	5.73-6.99	0.651	0.69	701	211
ISO_3	4.97-5.73	0.688	0.749	854	214
ISO_3	4.45-4.97	0.706	0.739	981	214
ISO_3	4.06-4.45	0.743	0.776	1085	215
ISO_3	3.76-4.06	0.754	0.786	1195	201
ISO_3	3.52-3.76	0.776	0.822	1291	222
ISO_3	3.32-3.52	0.791	0.835	1386	216
ISO_3	3.15-3.32	0.822	0.903	1465	210
ISO_3	3.01-3.15	0.833	0.883	1546	215
ISO_3	2.88-3.01	0.809	0.91	1629	213
ISO_3	2.77-2.88	0.696	0.796	1686	210
ISO_3	2.67-2.77	0.601	0.756	1768	211
ISO_3	2.58-2.67	0.497	0.621	1812	214
ISO_3	2.49-2.58	0.513	0.581	1831	196
ISO_3	2.42-2.49	0.593	0.724	1398	123
ISO_3	2.35-2.42	0	0	0	0
ISO_3	2.29-2.35	0	0	0	0
ISO_3	2.23-2.29	0	0	0	0
ANO_3	9.79-49.92	0.45	0	259	0
ANO_3	6.99-9.79	0.537	0	527	0
ANO_3	5.73-6.99	0.682	0	701	0
ANO_3	4.97-5.73	0.725	0	854	0
ANO_3	4.45-4.97	0.781	0	981	0
ANO_3	4.06-4.45	0.87	0	1085	0
ANO_3	3.76-4.06	0.888	0	1195	0
ANO_3	3.52-3.76	0.942	0	1291	0
ANO_3	3.32-3.52	0.97	0	1386	0
ANO_3	3.15-3.32	0.978	0	1465	0
ANO_3	3.01-3.15	0.991	0	1546	0
ANO_3	2.88-3.01	0.995	0	1629	0
ANO_3	2.77-2.88	0.997	0	1686	0
ANO_3	2.67-2.77	0.999	0	1768	0
ANO_3	2.58-2.67	0.999	0	1836	0
ANO_3	2.49-2.58	0.999	0	1899	0
ANO_3	2.42-2.49	1	0	1967	0
ANO_3	2.35-2.42	1	0	2023	0
ANO_3	2.29-2.35	1	0	2058	0
ANO_3	2.23-2.29	1	0	1738	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	114.994	39.457	3.413	PT	50.28	0.22
2	128.75	51.355	23.255	PT	92.19	0.11
3	113.771	54.747	34.67	PT	106.5	0.07
4	76.39	73.013	10.755	PT	80.89	0.02
5	-10.259	121.163	2.858	PT	83.39	0.02

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 32341

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
9.51-100	43.6	0.832	505
7.43-9.51	39.2	0.92	507
6.33-7.43	49.1	0.927	583
5.61-6.33	47.7	0.917	656
5.09-5.61	54.9	0.914	731
4.69-5.09	54.1	0.937	780
4.37-4.69	58.5	0.943	828
4.11-4.37	55.9	0.945	903
3.89-4.11	63	0.947	939
3.71-3.89	64.2	0.929	988
3.54-3.71	66.2	0.945	1024
3.4-3.54	68.9	0.936	1068
3.27-3.4	73.3	0.926	1118
3.16-3.27	72.7	0.932	1154
3.06-3.16	75.7	0.924	1184
2.96-3.06	76.5	0.931	1228
2.88-2.96	79.6	0.921	1265
2.8-2.88	79.6	0.915	1292
2.73-2.8	86.2	0.908	1328
2.66-2.73	82.1	0.898	1354
2.6-2.66	81.5	0.919	1399
2.54-2.6	84.9	0.908	1421
2.49-2.54	86.5	0.914	1454
2.44-2.49	88.8	0.942	1480
2.39-2.44	87.7	0.913	1508
2.34-2.39	87.5	0.908	1544
2.3-2.34	90	0.908	1579
2.23-2.3	90.4	0.835	2521

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Processing

Software

Name	Version	Classification
SCALA		data scaling
SHARP		phasing
DM	6	phasing
CNS		refinement
PDB_EXTRACT	2	data extraction
HKL-2000		data collection
MOSFLM		data reduction
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.53→40 Å / FOM work R set: 0.869 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.227	1041	4.8 %	RANDOM
R_work	0.177	-	-	-
all	0.1803	21876	-	-
obs	0.1803	21444	98 %	-

Solvent computation

B_sol: 28.246 Å²

Displacement parameters

B_iso mean: 21.017 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.31 Å	0.24 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	0.31 Å	0.22 Å

Refinement step

Cycle: LAST / Resolution: 2.53→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3661	0	84	297	4042

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_bond_d	0.006
X-RAY DIFFRACTION	c_angle_deg	1.3
X-RAY DIFFRACTION	c_mcbond_it	1.112	1.5
X-RAY DIFFRACTION	c_scbond_it	2.121	2
X-RAY DIFFRACTION	c_mcangle_it	1.782	2
X-RAY DIFFRACTION	c_scangle_it	3.191	2.5

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs
2.53-2.57	0.238	48	0.218	1001	1049
2.57-2.62	0.257	48	0.188	1020	1068
2.62-2.67	0.275	51	0.225	1007	1058
2.67-2.73	0.275	51	0.213	999	1050
2.73-2.78	0.293	62	0.214	999	1061
2.78-2.85	0.268	59	0.199	996	1055
2.85-2.92	0.274	39	0.211	1034	1073
2.92-3	0.284	49	0.214	1009	1058
3-3.09	0.263	56	0.205	1001	1057
3.09-3.19	0.197	57	0.172	1009	1066
3.19-3.3	0.228	62	0.174	1003	1065
3.3-3.43	0.27	49	0.189	1013	1062
3.43-3.59	0.221	48	0.181	1013	1061
3.59-3.78	0.211	49	0.162	1027	1076
3.78-4.02	0.2	47	0.147	1020	1067
4.02-4.32	0.182	45	0.142	1036	1081
4.32-4.76	0.145	51	0.114	1021	1072
4.76-5.45	0.161	44	0.151	1048	1092
5.45-6.86	0.232	52	0.2	1053	1105
6.86-40	0.238	74	0.186	1094	1168

Xplor file

Refine-ID	Serial no	Param file
X-RAY DIFFRACTION	1	CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION	2	CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION	3	dxc.par

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