PDB-5abm: Sheep aldehyde dehydrogenase 1A1

ID or keywords:

Entry

Database: PDB / ID: 5abm

Title

Sheep aldehyde dehydrogenase 1A1

Components

RETINAL DEHYDROGENASE 1

Keywords

OXIDOREDUCTASE / OXIDATION-REDUCTION PROCESS / ACTIVITY

Function / homology

Function and homology information

fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity ...
Similarity search - Function

Biological species

OVIS ARIES (sheep)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Koch, M.F. / Harteis, S. / Blank, I.D. / Pestel, G. / Tietze, L.F. / Ochsenfeld, C. / Schneider, S. / Sieber, S.A.

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition by Cytotoxic Duocarmycin Analogues.
Authors: Koch, M.F. / Harteis, S. / Blank, I.D. / Pestel, G. / Tietze, L.F. / Ochsenfeld, C. / Schneider, S. / Sieber, S.A.

History

Deposition	Aug 7, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 30, 2015	Group: Database references
Revision 1.2	Nov 18, 2015	Group: Database references
Revision 1.3	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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	5abm.cif.gz	780.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5abm.ent.gz	655.6 KB	Display	PDB format
PDBx/mmJSON format	5abm.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5abm_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	5abm_full_validation.pdf.gz	2 MB	Display
Data in XML	5abm_validation.xml.gz	84.2 KB	Display
Data in CIF	5abm_validation.cif.gz	122.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ab/5abm ftp://data.pdbj.org/pub/pdb/validation_reports/ab/5abm	HTTPS FTP

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Related structure data

Related structure data	5ac0C 5ac1C 5ac2C 4x4lS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1o9j-d 4fr8-2 2onp-1 5tei-1 3n82-1 5ac1-2 1o02-2 5l2o-2 7jwu-1 6dum-1 6b5g-d 1nzx-2 3inj-1 4kwg-1 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

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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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)

Deposited unit

A: RETINAL DEHYDROGENASE 1

B: RETINAL DEHYDROGENASE 1

C: RETINAL DEHYDROGENASE 1

D: RETINAL DEHYDROGENASE 1

hetero molecules

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

1

C: RETINAL DEHYDROGENASE 1

D: RETINAL DEHYDROGENASE 1

hetero molecules

C: RETINAL DEHYDROGENASE 1

D: RETINAL DEHYDROGENASE 1

hetero molecules

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

2

A: RETINAL DEHYDROGENASE 1

B: RETINAL DEHYDROGENASE 1

hetero molecules

A: RETINAL DEHYDROGENASE 1

B: RETINAL DEHYDROGENASE 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	187.985, 80.804, 171.408
Angle α, β, γ (deg.)	90.00, 117.97, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-2054- HOH

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (0.8264, 0.000412, 0.5632), (0.001694, -1, -0.001755), (0.5632, 0.002404, -0.826)
Vector: -33.3, 95.41, 107.8)

#1: Protein	RETINAL DEHYDROGENASE 1 / RALDH 1 / RALDH1 / ALDH-E1 / ALHDII / ALDEHYDE DEHYDROGENASE FAMILY 1 MEMBER A1 / ALDEHYDE ...RALDH 1 / RALDH1 / ALDH-E1 / ALHDII / ALDEHYDE DEHYDROGENASE FAMILY 1 MEMBER A1 / ALDEHYDE DEHYDROGENASE / CYTOSOLIC / ALDEHYDE DEHYDROGENASE 1A1 Mass: 54754.391 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-501 Source method: isolated from a genetically manipulated source Source: (gene. exp.) OVIS ARIES (sheep) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51977, retinal dehydrogenase
#2: Chemical	ChemComp-TXE / [[(2R,3S,4R,5R)-5-[(3R)-3-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-ph osphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate / 1,2,3,4-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE Mass: 667.457 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₁N₇O₁₄P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1340 / 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: 2.62 Å³/Da / Density % sol: 26.2 % / Description: NONE
Crystal grow	Temperature: 277 K Details: 100 MM BIS-TRIS, PH 6.0, 4.5-7% PEG5000, 150=225MM MGCL2, 4DEGREE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.7→51.8 Å / Num. obs: 249604 / % possible obs: 99.7 % / Observed criterion σ(I): 12.6 / Redundancy: 6.7 % / R_merge(I) obs: 0.11 / Net I/σ(I): 12.6
Reflection shell	Resolution: 1.7→1.76 Å / R_merge(I) obs: 0.86 / Mean I/σ(I) obs: 2.1 / % possible all: 97.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4X4L

4x4l

Resolution: 1.7→151.85 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.948 / SU B: 4.268 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20268	12505	5 %	RANDOM
R_work	0.18013	-	-	-
obs	0.18126	237099	99.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 22.184 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.1 Å²	0 Å²	0.52 Å²
2-	-	-0.01 Å²	0 Å²
3-	-	-	-1.05 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→151.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15225	0	180	1340	16745

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	16043
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	15189
X-RAY DIFFRACTION	r_angle_refined_deg	1.81	1.975	21762
X-RAY DIFFRACTION	r_angle_other_deg	1.311	3	35143
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.557	5	2036
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.991	24.853	682
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.731	15	2750
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.276	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	2361
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	18295
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	3601
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.751	0.908	8036
X-RAY DIFFRACTION	r_mcbond_other	0.751	0.908	8035
X-RAY DIFFRACTION	r_mcangle_it	1.124	1.359	10084
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.507	1.109	8007
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.697→1.741 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.377	881	-
R_work	0.372	16877	-
obs	-	-	96.33 %

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	1.8531	-0.2006	-0.2625	1.4923	-0.169	2.2079	-0.0244	-0.162	-0.2003	0.0925	0.0341	-0.0793	0.176	0.0745	-0.0097	0.0801	0.0146	-0.1073	0.0165	0.0034	0.1988	80.4556	15.6211	86.7508
2	0.5865	-0.1888	0.2809	0.8198	-0.3583	0.3698	-0.0041	-0.0219	-0.0602	0.0541	0.0299	-0.0233	-0.0187	-0.0161	-0.0258	0.0537	0.0054	-0.0699	0.0114	-0.006	0.1004	71.2616	30.5814	79.5716
3	2.2234	-1.396	-0.7938	2.4285	0.8963	1.5108	-0.2569	-0.7261	-0.1461	0.2884	0.3358	0.0228	0.2102	0.2125	-0.0789	0.1494	0.0817	-0.0841	0.3189	0.0608	0.0996	68.9381	32.5286	111.4767
4	2.4815	-0.393	-0.8285	0.8297	-0.2219	1.0323	0.0135	-0.3366	0.074	0.1209	0.0668	-0.031	-0.0634	0.0376	-0.0803	0.0961	0.0084	-0.0834	0.0817	-0.0104	0.0956	61.4292	46.1744	101.0364
5	7.4254	3.3378	-2.4267	1.5073	-1.1556	2.0853	-0.0157	0.1912	0.0207	-0.0132	0.0689	0.0004	-0.1177	-0.1166	-0.0532	0.1717	0.0224	0.0065	0.1801	0.0165	0.1608	61.9712	41.7843	79.7503
6	0.8865	-0.5682	0.6805	1.866	-0.6748	0.9974	-0.0758	0.0605	0.0891	0.0583	0.0266	-0.0518	-0.0966	-0.0055	0.0491	0.0511	-0.0028	-0.0642	0.036	0.0082	0.0916	62.6829	52.5981	60.6553
7	0.9114	0.7568	2.8971	0.7295	1.9155	17.6238	-0.1407	0.2357	0.0665	-0.2708	0.2114	0.0901	-0.359	-0.0022	-0.0708	0.3183	0.0168	-0.0729	0.1416	0.0354	0.2199	75.3922	86.1024	72.1789
8	2.2139	1.0434	-0.0979	1.0133	0.0218	0.98	0.0181	-0.151	0.1808	0.0839	-0.0505	-0.0266	-0.0964	0.0926	0.0323	0.0923	-0.0035	-0.1055	0.0185	-0.0166	0.1449	76.2778	72.1566	88.8484
9	0.6237	0.4335	-0.0631	0.8745	-0.2645	0.1447	-0.0725	0.0543	0.0362	-0.0832	0.0435	-0.0542	0.023	0.0001	0.029	0.0798	0.0003	-0.0787	0.0113	-0.0067	0.1042	71.1805	64.7175	80.4811
10	0.7276	0.5762	0.1183	1.8689	0.5385	1.3496	-0.0788	0.2153	0.0395	-0.17	0.0677	-0.0609	-0.1243	0.1853	0.0111	0.0891	-0.0444	-0.0364	0.1491	0.0304	0.1398	83.9065	63.2238	54.0913
11	1.3018	0.5998	0.152	1.0464	-0.1325	1.2674	-0.0583	0.1695	-0.006	-0.1102	0.0632	-0.1312	0.0083	0.1846	-0.0049	0.0729	-0.0048	-0.0571	0.0824	0.0014	0.1234	80.5845	54.3878	58.3472
12	5.1384	3.0818	-0.5885	2.9166	-0.2501	0.0788	-0.1539	0.1966	-0.0334	-0.118	0.1572	-0.0857	0.0172	-0.0269	-0.0033	0.0763	-0.005	-0.0733	0.0511	0.0029	0.0868	53.8936	43.8836	91.607
13	2.1818	0.6808	-0.3719	1.2885	0.2884	1.9554	-0.0726	0.1752	-0.3271	-0.0866	0	-0.0204	0.186	-0.0152	0.0726	0.1313	0.0061	-0.1136	0.0177	-0.036	0.1912	87.4363	25.4282	131.0133
14	0.3014	0.0384	0.2326	0.78	0.4688	0.6617	0.038	0.0112	-0.0515	-0.05	-0.001	-0.0089	-0.0209	0.0244	-0.0371	0.0676	0.0004	-0.0813	0.0169	-0.0067	0.1074	92.8547	40.631	141.1436
15	0.8794	0.5975	0.1769	1.651	0.4332	1.1484	0.0183	0.213	-0.0941	-0.1642	0.0167	-0.2403	-0.0463	0.1962	-0.035	0.1407	0.0297	-0.0556	0.1652	-0.036	0.111	114.5323	46.8089	115.4741
16	1.5195	0.6417	-1.0302	3.0983	-1.1992	1.5608	-0.026	0.4087	-0.1555	-0.2454	-0.0338	-0.0063	-0.0184	-0.056	0.0599	0.1586	0.0284	-0.0978	0.219	-0.1046	0.1061	101.576	36.7142	110.6448
17	1.4035	0.1627	0.0915	0.8589	0.5561	1.1081	0.0227	0.2178	-0.0021	-0.1317	-0.0004	-0.0274	-0.0541	0.011	-0.0222	0.1167	0.0351	-0.0799	0.0883	-0.0028	0.0898	107.324	51.5326	120.7115
18	1.0997	1.437	1.9287	3.2187	2.5401	3.4085	-0.0474	0.104	-0.0287	-0.1012	0.1212	-0.0413	-0.0879	0.2199	-0.0738	0.069	-0.0085	-0.0587	0.0725	-0.029	0.0969	94.2391	61.5548	160.0748
19	1.5736	-0.4627	-0.2646	1.5443	-0.2534	1.9889	-0.0091	-0.0191	0.1581	-0.0106	-0.0108	0.158	-0.1735	-0.1416	0.02	0.1396	0.0261	-0.134	0.0186	-0.0181	0.1776	83.6814	89.7805	135.1716
20	0.6335	-0.3884	0.1887	0.9104	0.04	0.221	-0.0393	-0.0258	0.0271	0.0134	-0.0095	0.079	-0.0235	-0.0026	0.0489	0.0944	0.0085	-0.0851	0.0203	-0.0004	0.0938	94.7358	74.8434	138.9677
21	0.8793	0.0066	-0.0042	1.8122	-0.5958	1.4152	-0.0139	-0.2276	0.1357	0.1718	0.0251	0.2537	-0.1924	-0.3501	-0.0112	0.1257	0.0573	-0.032	0.2189	-0.0582	0.2128	70.3312	73.2696	159.7478
22	1.2425	-0.5705	0.2807	0.9205	-0.1461	1.5848	-0.0358	-0.1074	-0.0009	0.0747	0.0286	0.1937	-0.0162	-0.2907	0.0072	0.0827	-0.0026	-0.0601	0.1119	-0.0278	0.1491	77.2022	63.2424	157.3918
23	0.1218	-0.1721	1.0025	0.3929	-2.1221	11.7289	-0.0236	-0.0079	-0.0229	-0.1311	-0.0986	-0.043	0.6757	0.314	0.1222	0.2572	0.0446	0.0443	0.2367	0.0251	0.2653	98.5529	64.4312	144.6457
24	2.274	-1.1586	0.0444	1.9131	-0.393	0.9335	0.0924	0.0809	-0.1602	-0.0711	-0.0358	0.0548	0.0326	0.0926	-0.0565	0.0922	0.0125	-0.0764	0.0269	-0.0113	0.0735	116.7544	51.646	135.3324

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 57
2	X-RAY DIFFRACTION	2	A	58 - 269
3	X-RAY DIFFRACTION	3	A	270 - 407
4	X-RAY DIFFRACTION	4	A	408 - 478
5	X-RAY DIFFRACTION	5	A	479 - 484
6	X-RAY DIFFRACTION	6	A	485 - 500
7	X-RAY DIFFRACTION	7	B	7 - 20
8	X-RAY DIFFRACTION	8	B	21 - 86
9	X-RAY DIFFRACTION	9	B	87 - 269
10	X-RAY DIFFRACTION	10	B	270 - 362
11	X-RAY DIFFRACTION	11	B	363 - 482
12	X-RAY DIFFRACTION	12	B	483 - 500
13	X-RAY DIFFRACTION	13	C	7 - 56
14	X-RAY DIFFRACTION	14	C	57 - 270
15	X-RAY DIFFRACTION	15	C	271 - 327
16	X-RAY DIFFRACTION	16	C	328 - 372
17	X-RAY DIFFRACTION	17	C	373 - 482
18	X-RAY DIFFRACTION	18	C	483 - 500
19	X-RAY DIFFRACTION	19	D	7 - 57
20	X-RAY DIFFRACTION	20	D	58 - 269
21	X-RAY DIFFRACTION	21	D	270 - 375
22	X-RAY DIFFRACTION	22	D	376 - 479
23	X-RAY DIFFRACTION	23	D	480 - 485
24	X-RAY DIFFRACTION	24	D	486 - 500

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