PDB-5ovk: Crystal structure MabA bound to NADPH from M. smegmatis

ID or keywords:

Entry

Database: PDB / ID: 5ovk

Title

Crystal structure MabA bound to NADPH from M. smegmatis

Components

3-oxoacyl-[acyl-carrier-protein] reductase FabG

Keywords

OXIDOREDUCTASE / FabG / SDR / beta-keto-acyl-acp-reductase

Function / homology

Function and homology information

acetoacetyl-CoA reductase /

acetoacetyl-CoA reductase activity / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation /

NADP binding / extracellular region
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Kussau, T. / Van Wyk, N. / Viljoen, A. / Olieric, V. / Flipo, M. / Kremer, L. / Blaise, M.

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structural rearrangements occurring upon cofactor binding in the Mycobacterium smegmatis beta-ketoacyl-acyl carrier protein reductase MabA.
Authors: Kussau, T. / Flipo, M. / Van Wyk, N. / Viljoen, A. / Olieric, V. / Kremer, L. / Blaise, M.

History

Deposition	Aug 29, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2018	Group: Data collection / Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 17, 2024	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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Download

PDBx/mmCIF format	5ovk.cif.gz	366.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ovk.ent.gz	300.5 KB	Display	PDB format
PDBx/mmJSON format	5ovk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ov/5ovk ftp://data.pdbj.org/pub/pdb/validation_reports/ov/5ovk	HTTPS FTP

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Related structure data

Related structure data	5ovjC 5ovlSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4cqm-2 4cql-2 4cql-4 1uzn-1 6uut-d 4cql-1 4cqm-3 4rf2-1 1uzl-1 4eds-3 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	#216 - Dec 2017 Biodegradable Plastic similarity (3) #90 - Jun 2007 Fatty Acid Synthase similarity (4) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

C: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

D: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	59.190, 69.350, 106.940
Angle α, β, γ (deg.)	90.00, 91.85, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	3-oxoacyl-[acyl-carrier-protein] reductase FabG / 3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta- ...3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta-ketoacyl-ACP reductase Mass: 26729.258 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: fabG, MSMEG_3150, MSMEI_3069 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): rosetta 2 pLysS References: UniProt: P71534, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 881 / 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: 2.05 Å³/Da / Density % sol: 40.05 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-TRIS pH 5.5, 0.2 M NaCl and 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 26, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.45→39.034 Å / Num. obs: 138568 / % possible obs: 89.07 % / Redundancy: 6.7 % / R_rim(I) all: 0.097 / Net I/σ(I): 14.83
Reflection shell	Resolution: 1.45→1.502 Å / Mean I/σ(I) obs: 1.05 / Num. unique obs: 12845 / R_rim(I) all: 1.75 / % possible all: 84.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5OVL

5ovl

Resolution: 1.45→39.034 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1969	2007	1.47 %
R_work	0.1722	-	-
obs	0.1725	136349	89.08 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.45→39.034 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6802	0	137	881	7820

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7095
X-RAY DIFFRACTION	f_angle_d	0.76	9606
X-RAY DIFFRACTION	f_dihedral_angle_d	18.692	2536
X-RAY DIFFRACTION	f_chiral_restr	0.07	1077
X-RAY DIFFRACTION	f_plane_restr	0.004	1259

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 (%)
1.4499-1.4862	0.515	121	0.4974	8400	X-RAY DIFFRACTION	79
1.4862-1.5263	0.2933	172	0.3024	10685	X-RAY DIFFRACTION	100
1.5263-1.5713	0.2551	152	0.242	10760	X-RAY DIFFRACTION	100
1.5713-1.622	0.2695	158	0.2273	10676	X-RAY DIFFRACTION	100
1.622-1.68	0.2369	161	0.2075	10747	X-RAY DIFFRACTION	100
1.68-1.7472	0.2272	161	0.2028	10783	X-RAY DIFFRACTION	100
1.7472-1.8267	0.2248	159	0.1786	10717	X-RAY DIFFRACTION	100
1.8267-1.923	0.2364	109	0.1825	7233	X-RAY DIFFRACTION	99
1.923-2.0435	0.1846	76	0.1617	5247	X-RAY DIFFRACTION	99
2.0435-2.2013	0.1933	168	0.16	10723	X-RAY DIFFRACTION	100
2.2013-2.4228	0.1934	106	0.1588	7383	X-RAY DIFFRACTION	69
2.4228-2.7733	0.1788	159	0.1518	10850	X-RAY DIFFRACTION	100
2.7733-3.4937	0.1673	151	0.1465	10129	X-RAY DIFFRACTION	94
3.4937-39.0477	0.1555	154	0.1385	10009	X-RAY DIFFRACTION	91

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	0.7926	0.6262	0.3243	2.7564	-0.9989	1.4739	-0.0178	0.0351	-0.0047	-0.2902	-0.0465	-0.1649	0.1307	0.0837	0.0878	0.1647	0.0037	0.0081	0.0901	-0.0185	0.1256	15.2066	3.7171	14.9031
2	0.6719	2.1193	-1.4244	9.0656	-3.8878	3.1545	-0.1898	0.2685	-0.0017	-0.9376	0.2488	0.2904	0.4132	-0.3525	-0.0462	0.3467	-0.0254	-0.0398	0.2179	-0.0263	0.1721	10.2024	7.1365	1.2177
3	2.7064	4.1462	-0.8965	8.0734	-1.7239	1.0512	-0.0352	0.0307	-0.0644	-0.3332	-0.0015	-0.2435	0.0433	0.0827	0.05	0.1851	0.0296	0.0189	0.1387	-0.0204	0.1271	21.4608	23.6017	5.6879
4	4.8321	5.9389	-4.171	8.1222	-3.9024	5.402	-0.0491	0.4127	0.3354	-0.385	0.2195	0.7099	0.1946	-0.572	-0.1146	0.1805	-0.0003	-0.0776	0.1681	-0.0088	0.1939	3.0718	14.4994	7.2339
5	4.1937	4.8753	0.4859	6.0933	0.2066	0.9493	-0.0531	0.0446	0.1104	-0.0639	0.0168	0.0956	0.0078	0.022	0.0442	0.1249	0.0307	0.0029	0.1143	-0.0097	0.1343	15.7412	21.1348	17.1354
6	8.4922	3.8718	-4.3985	3.0871	-1.7653	3.1761	-0.0396	0.1981	0.0622	-0.1179	0.0628	0.1207	0.0569	-0.1634	-0.0315	0.1161	0.018	-0.0251	0.0802	-0.0081	0.0901	9.3183	24.5068	14.7052
7	4.8798	1.4342	-0.1351	3.7979	-0.0451	2.9258	0.033	0.5289	-0.111	-0.2517	-0.0225	-0.7308	0.1392	0.6589	-0.0418	0.1993	0.0241	0.041	0.2526	-0.0032	0.1833	25.8796	16.6915	17.2751
8	2.5225	-0.3814	-0.7437	1.0002	-1.2405	2.174	-0.1163	0.3696	0.2103	-0.3419	0.2739	-0.9913	-0.2029	0.888	-0.0796	0.2209	-0.0521	0.0798	0.3915	-0.0085	0.3802	35.7133	21.1468	24.568
9	0.6092	0.2179	-0.2809	1.4734	0.1385	0.6119	-0.0521	0.0292	-0.0764	-0.1176	0.0312	0.0041	0.0834	-0.0316	0.0218	0.1401	-0.0028	-0.0041	0.1379	0.001	0.1216	15.3395	16.4555	25.0689
10	1.4377	-1.1134	-0.2572	3.9993	1.791	4.248	-0.1224	-0.0145	-0.1501	0.0671	0.009	0.0754	0.1602	0.0857	0.1598	0.0878	-0.0331	-0.0061	0.0656	0.0057	0.1194	16.4606	6.8545	39.0351
11	0.4275	-0.3554	-0.2879	2.2629	1.7422	3.8213	-0.0096	-0.0407	-0.0519	0.2538	-0.008	0.2053	0.259	-0.2256	0.0054	0.1776	-0.0279	0.0197	0.1508	0.0195	0.1784	8.2583	7.6585	46.7386
12	0.3896	-1.3075	-1.2136	9.1065	4.1359	3.7933	-0.1009	-0.0955	-0.0582	0.5742	0.0856	-0.0331	0.2216	0.1655	0.0358	0.1602	0.0077	0.0019	0.1716	0.0319	0.1305	16.5012	13.889	56.4456
13	2.493	-4.1306	-0.1142	8.1099	0.0934	0.8738	-0.0401	-0.0539	-0.092	0.2177	0.0295	0.3641	-0.1288	-0.1303	0.0134	0.0946	-0.0145	0.027	0.1529	-0.0009	0.1261	6.4421	29.4194	47.7603
14	7.6249	-4.6212	-3.3037	6.0626	2.71	4.397	0.0146	-0.3301	0.133	0.2479	0.0728	-0.4822	0.1441	0.4636	-0.0587	0.1097	-0.0152	-0.0392	0.1546	0.019	0.1378	23.8006	19.4797	49.0518
15	1.9745	-1.9198	1.5998	3.5969	-1.417	1.83	0.0364	0.0247	0.0962	0.001	-0.0764	-0.0228	0.0117	-0.0086	0.0255	0.074	-0.0123	0.0241	0.1078	0.0077	0.11	11.4845	24.457	37.5277
16	1.8986	-1.652	-1.0725	2.6983	0.4289	1.5875	-0.0327	-0.0551	0.0894	0.0283	0.0187	-0.0811	0.0173	0.0853	0.0062	0.1052	-0.0151	-0.003	0.1146	0.0025	0.0989	18.6505	27.3078	39.0639
17	4.2235	0.6116	2.4189	1.3903	-0.4066	3.5684	-0.1153	-0.1637	0.0936	-0.0341	0.0905	0.3188	-0.0882	-0.4655	0.0514	0.1278	0.0067	0.0212	0.1319	-0.0105	0.1647	2.299	20.877	32.3877
18	0.0804	-0.0095	0.0511	1.4791	-0.2668	0.7265	0.0196	-0.0174	0.0109	-0.0485	-0.0112	0.055	0.0826	-0.0055	-0.0076	0.1059	-0.0084	0.0053	0.1349	-0.014	0.1173	12.104	17.3196	30.9468
19	0.9322	-0.2639	0.2376	1.8487	0.1614	2.0795	0.014	-0.0137	-0.0155	-0.2252	-0.0715	0.1403	-0.2468	-0.119	0.1	0.2075	0.0115	0.011	0.114	0.0015	0.1422	15.8472	55.7603	12.3512
20	1.6528	-1.6568	-0.7618	4.5266	-0.6964	1.4053	0.1444	0.3011	0.1638	-0.4432	-0.0427	0.6303	-0.1413	-0.3421	0.0524	0.2843	0.0171	-0.028	0.231	0.041	0.2097	12.9361	55.3523	1.0413
21	1.1914	0.8197	-0.4471	2.4542	-0.4706	1.3931	-0.0671	0.1342	0.0062	-0.3099	0.0742	0.0168	-0.0333	-0.0645	-0.01	0.1518	0.029	-0.0068	0.115	0.0016	0.0997	16.1904	40.5063	4.3957
22	0.2067	-0.1352	-0.0304	1.4184	-0.0207	0.9766	0.0175	-0.0104	0.0061	-0.0754	-0.0107	0.1324	-0.0668	-0.0637	-0.005	0.1298	0.0038	-0.0045	0.118	0.0039	0.1137	12.6804	41.7847	18.4623
23	2.6936	-2.1187	1.7738	3.1779	-3.503	4.6517	0.0258	0.0435	0.081	0.0031	-0.001	0.0168	-0.0543	-0.1434	-0.0411	0.1857	-0.0136	0.0325	0.0773	-0.0222	0.1431	11.4408	58.5692	32.287
24	0.9197	-0.5724	0.1522	3.0859	-2.9826	4.1781	0.0283	-0.1053	0.0378	0.1524	-0.0539	-0.173	-0.3384	0.1189	0.0403	0.189	-0.0391	0.0103	0.1387	-0.0324	0.1509	19.1832	59.3084	41.0696
25	0.3545	-0.212	0.5501	7.8986	-3.9766	3.2692	0.0019	-0.1656	0.1395	0.4997	0.095	0.1223	-0.4041	-0.1506	-0.0683	0.2456	0.0089	0.0434	0.1573	-0.0485	0.154	9.7236	55.9597	50.8911
26	2.9682	-3.5076	1.5927	4.2811	-2.0925	1.1223	-0.0216	-0.0607	0.0978	0.1423	-0.0316	-0.1959	-0.0369	0.0916	0.0688	0.1462	-0.0155	-0.0168	0.1497	-0.0121	0.1438	19.9646	38.8953	47.3198
27	4.0176	-2.431	3.859	4.2364	-3.7182	7.4332	-0.0514	-0.2787	-0.1179	0.2346	0.2057	0.5194	-0.2163	-0.5827	-0.1262	0.1244	-0.004	0.0396	0.1341	-0.0159	0.1599	2.5679	48.7922	44.2221
28	3.6188	-3.7306	-0.7616	5.1808	0.3293	1.1368	0.072	0.067	-0.1587	0.0431	-0.1071	0.1587	-0.0785	0.0119	0.0285	0.0868	-0.0218	-0.0005	0.1023	-0.0105	0.1073	15.3839	41.9268	35.4085
29	4.8813	-2.7597	3.4157	2.9613	-2.0544	3.55	-0.0325	-0.1042	-0.0012	0.0416	0.0372	0.1663	-0.0959	-0.1214	0.0127	0.0914	-0.0081	0.0156	0.0889	-0.0172	0.0959	8.713	38.7824	37.1386
30	3.521	-1.1286	-1.3691	2.9324	-0.2691	2.0101	-0.0969	-0.4713	0.1304	0.1566	0.0353	-0.2942	-0.1833	0.2991	0.0874	0.135	-0.0283	-0.0135	0.1482	-0.0279	0.1004	19.5876	45.5972	34.0758
31	4.6404	1.147	-0.385	6.5063	2.4207	7.5553	-0.0596	-0.2915	-0.2968	0.2908	0.2949	-0.9803	0.3415	0.7818	-0.2439	0.1477	0.0016	-0.0176	0.2477	0.0111	0.2135	33.0611	41.5123	27.7716
32	0.6145	-0.2088	-0.1641	1.0085	-0.061	0.6757	0.0409	-0.0109	0.0625	0.0008	-0.0298	-0.0358	-0.1277	-0.0033	-0.0103	0.1412	-0.0133	0.0004	0.1314	-0.005	0.1131	16.1997	46.4216	27.4058

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 63 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 64 through 87 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 88 through 121 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 122 through 138 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 139 through 158 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 159 through 182 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 183 through 203 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 204 through 221 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 222 through 255 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 14 through 33 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 34 through 63 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 64 through 87 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 88 through 121 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 122 through 138 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 139 through 158 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 159 through 182 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 183 through 221 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 222 through 255 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 14 through 46 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 47 through 63 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 64 through 158 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 159 through 255 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 14 through 33 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 34 through 63 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 64 through 87 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 88 through 121 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 122 through 138 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 139 through 158 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 159 through 182 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 183 through 197 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 198 through 221 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 222 through 255 )

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