PDB-5u0m: Fatty aldehyde dehydrogenase from Marinobacter aquaeolei VT8 and ...

ID or keywords:

Entry

Database: PDB / ID: 5u0m

Title

Fatty aldehyde dehydrogenase from Marinobacter aquaeolei VT8 and cofactor complex

Components

N-succinylglutamate 5-semialdehyde dehydrogenase

Keywords

OXIDOREDUCTASE / Dehydrogenase

Function / homology

Function and homology information

succinylglutamate-semialdehyde dehydrogenase / succinylglutamate-semialdehyde dehydrogenase activity / arginine catabolic process to succinate / arginine catabolic process to glutamate
Similarity search - Function

Biological species

Marinobacter hydrocarbonoclasticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.075 Å

Authors

Shi, K. / Mulliner, K. / Barney, B.M. / Aihara, H.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM118047	United States
National Science Foundation (NSF, United States)	CBET-1437758	United States

Citation

Journal: Appl. Environ. Microbiol. / Year: 2017
Title: Five Fatty Aldehyde Dehydrogenase Enzymes from Marinobacter and Acinetobacter spp. and Structural Insights into the Aldehyde Binding Pocket.
Authors: Bertram, J.H. / Mulliner, K.M. / Shi, K. / Plunkett, M.H. / Nixon, P. / Serratore, N.A. / Douglas, C.J. / Aihara, H. / Barney, B.M.

History

Deposition	Nov 24, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 26, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jun 14, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.title
Revision 1.2	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Apr 18, 2018	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / diffrn_detector ...chem_comp / diffrn_detector / entity / pdbx_entity_nonpoly Item: _chem_comp.name / _diffrn_detector.detector ..._chem_comp.name / _diffrn_detector.detector / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.4	Nov 27, 2019	Group: Author supporting evidence / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / pdbx_entity_nonpoly Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Revision 1.5	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5u0m.cif.gz	384.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5u0m.ent.gz	317.4 KB	Display	PDB format
PDBx/mmJSON format	5u0m.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5u0m_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	5u0m_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5u0m_validation.xml.gz	41.8 KB	Display
Data in CIF	5u0m_validation.cif.gz	55 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u0/5u0m ftp://data.pdbj.org/pub/pdb/validation_reports/u0/5u0m	HTTPS FTP

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Related structure data

Related structure data	5u0lC 3ju8S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5u0l-d 4h7n-1 4mpb-1 4nmk-3 4nmk-2 4nmj-3 4nea-2 4h7n-2 4nmj-2 4go3-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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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: N-succinylglutamate 5-semialdehyde dehydrogenase

B: N-succinylglutamate 5-semialdehyde dehydrogenase

hetero molecules

109 kDa, 2 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)	99.347, 99.347, 254.425
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	N-succinylglutamate 5-semialdehyde dehydrogenase / Succinylglutamic semialdehyde dehydrogenase / SGSD Mass: 53368.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinobacter hydrocarbonoclasticus (strain ATCC 700491 / DSM 11845 / VT8) (bacteria) Strain: ATCC 700491 / DSM 11845 / VT8 / Gene: astD, Maqu_3316 / Production host: Escherichia coli (E. coli) References: UniProt: A1U5W8, succinylglutamate-semialdehyde dehydrogenase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.94 Å³/Da / Density % sol: 58.23 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium citrate, 20% w/v PEG2000 MME, 0.1M Imidazole, pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.08→92.573 Å / Num. obs: 23394 / % possible obs: 98.8 % / Redundancy: 14.2 % / CC_1/2: 0.991 / R_merge(I) obs: 0.528 / Net I/σ(I): 7.1
Reflection shell	Resolution: 3.09→3.3 Å / Redundancy: 13.4 % / R_merge(I) obs: 3.73 / Mean I/σ(I) obs: 0.8 / CC_1/2: 0.534 / % possible all: 93.3

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Processing

Software

Name	Version	Classification
PHENIX	dev_2706	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3JU8

3ju8

Resolution: 3.075→34.794 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2731	1152	4.93 %
R_work	0.2191	-	-
obs	0.2218	23371	95.19 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.075→34.794 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7350	0	126	33	7509

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7643
X-RAY DIFFRACTION	f_angle_d	0.682	10395
X-RAY DIFFRACTION	f_dihedral_angle_d	7.969	4592
X-RAY DIFFRACTION	f_chiral_restr	0.043	1151
X-RAY DIFFRACTION	f_plane_restr	0.005	1364

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 (%)
3.0752-3.2151	0.4335	98	0.388	1925	X-RAY DIFFRACTION	67
3.2151-3.3845	0.4039	132	0.3348	2734	X-RAY DIFFRACTION	96
3.3845-3.5963	0.3692	149	0.3017	2841	X-RAY DIFFRACTION	99
3.5963-3.8737	0.3189	143	0.2722	2858	X-RAY DIFFRACTION	100
3.8737-4.2629	0.2879	152	0.2141	2896	X-RAY DIFFRACTION	100
4.2629-4.8783	0.2192	148	0.1704	2900	X-RAY DIFFRACTION	100
4.8783-6.1406	0.242	163	0.1848	2942	X-RAY DIFFRACTION	100
6.1406-34.7967	0.2185	167	0.1692	3123	X-RAY DIFFRACTION	100

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	0.4376	0.4123	0.0205	0.3234	0.169	0.4391	0.0437	-0.2699	0.4352	0.1204	-0.0435	-0.286	-0.1564	0.2065	-0	0.7674	-0.0298	-0.0168	0.6472	-0.0362	0.5622	39.8882	12.3787	57.094
2	0.0726	-0.2428	-0.1588	0.2373	-0.2481	0.5504	0.3464	0.2756	-0.2772	-0.0757	-0.378	0.3827	0.347	-0.5794	-0.0401	0.7569	-0.1076	-0.0508	0.5268	0.1203	0.6274	29.9051	-1.6648	52.488
3	0.7149	-0.1375	0.1461	-0.0624	-0.0216	0.3719	-0.0249	-0.1476	0.0318	0.0803	0.0334	0.0465	0.166	0.1062	0	0.5249	0.0139	-0.0146	0.2977	-0.0032	0.4834	40.787	1.4343	44.7091
4	0.8557	-0.2232	0.1294	0.5989	0.1209	0.2799	0.1452	0.0754	-0.0605	0.0273	-0.0753	-0.009	-0.3794	-0.5372	0.0022	0.4427	0.0499	-0.026	0.3417	0.012	0.3846	19.2057	13.8276	26.8014
5	0.4977	0.144	-0.2397	0.1189	0.1022	0.1203	0.0531	0.0265	-0.154	-0.1659	0.0518	0.0693	0.1084	-0.1624	-0	0.6031	0.1097	0.0315	0.4476	0.106	0.6143	24.9012	18.3207	22.1444
6	0.1941	-0.2009	0.1279	0.2405	-0.0642	0.1995	-0.0564	0.1986	-0.0444	-0.1372	0.1338	0.1577	0.1371	0.3304	-0	0.5995	-0.0726	-0.0876	0.4329	-0.0114	0.5856	28.8734	0.2205	20.3015
7	0.3208	-0.1816	0.0077	0.281	-0.2548	-0.1849	-0.2194	-0.7027	0.0722	0.0624	0.4623	0.0474	0.2055	-0.0653	0.0414	0.7316	0.1015	-0.0612	0.4361	0.0299	0.3901	53.9663	-14.8002	36.5513
8	-0.0064	0.0061	-0.0258	0.3146	-0.1022	0.0361	0.1816	0.0849	0.2325	-0.1362	-0.058	-0.2812	-0.4236	0.1113	-0.0001	0.5431	0.052	0.0085	0.7836	0.0266	0.5438	72.4997	-5.1759	8.3615
9	1.1209	-0.7848	-0.4682	0.0107	0.0901	0.419	-0.0404	-0.1126	-0.1482	-0.148	-0.0769	0.2419	0.354	0.2944	-0.0251	0.7409	0.1008	-0.0232	0.436	0.0295	0.5088	57.4991	-14.7972	15.6002
10	0.0635	-0.016	0.0767	-0.0867	-0.1417	0.5658	0.2933	-0.1206	0.0501	0.016	-0.0946	0.2356	0.0378	0.354	0.0077	0.6954	0.0034	-0.0938	0.5686	-0.0988	0.5346	44.2347	-9.1658	23.8262
11	0.0883	-0.0088	0.0105	-0.043	0.0108	-0.0105	-0.144	0.6437	-0.1969	-0.0031	0.1179	-0.0962	0.3311	0.4405	0.0001	0.4977	0.0872	-0.0156	0.4794	-0.0261	0.4374	59.8053	-10.4843	14.1048
12	0.0371	0.1837	0.194	0.1002	0.2284	0.3494	0.1077	-0.5023	0.2714	-0.3845	-0.1728	-0.0971	-0.7682	0.2379	-0.0017	0.4338	0.0811	0.0452	0.5365	0.0169	0.5374	59.5181	2.8922	23.1795
13	0.351	0.2892	0.1063	0.1824	0.0851	0.0961	-0.2207	-0.4544	-0.1299	0.653	0.2069	0.1637	0.1077	-0.3275	-0.0002	0.8418	0.319	-0.0763	0.8796	0.1391	0.504	74.9836	-21.2695	43.9509
14	0.0095	0.1276	0.105	0.2047	0.096	0.1874	-0.1009	0.5487	0.0697	-0.3726	-0.2552	-0.3083	0.2189	-0.0853	-0.0221	0.729	0.1734	-0.1862	1.1032	0.033	0.7548	83.536	-13.7591	30.4053
15	0.2064	0.1679	-0.0349	0.6153	-0.0155	0.122	0.1317	-0.0907	0.1043	0.2527	-0.1256	-0.2769	0.3315	0.2601	0.0045	0.7098	0.2565	-0.2631	1.2963	0.0592	0.7162	79.6025	-11.6895	43.4372
16	0.3348	0.1281	-0.2278	0.0531	-0.1327	0.4651	-0.2117	-0.6743	-0.0561	-0.1628	-0.189	0.4911	-0.293	0.4652	0.0107	0.7826	0.1663	-0.0254	0.6245	0.0934	0.6557	62.0637	-17.7792	45.8286
17	0.1608	-0.3621	0.1562	-0.1061	0.1683	-0.041	-0.0147	0.3161	-0.0698	0.2139	-0.1414	0.1269	0.0817	0.1051	-0	0.5357	-0.0376	0.0091	0.4195	0.0648	0.6529	35.782	-4.8037	29.7008

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 58 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 95 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 96 through 253 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 254 through 345 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 346 through 400 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 401 through 443 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 444 through 490 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 4 through 40 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 41 through 120 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 121 through 153 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 154 through 198 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 199 through 248 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 249 through 309 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 310 through 345 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 346 through 400 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 401 through 443 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 444 through 490 )

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