PDB-5ovl: crystal structure of MabA bound to NADP+ from M. smegmatis

ID or keywords:

Entry

Database: PDB / ID: 5ovl

Title

crystal structure of MabA bound to NADP+ from M. smegmatis

Components

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

Keywords

OXIDOREDUCTASE / FabG / beta-keto-acyl-acp / FAS II

Function / homology

Function and homology information

acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / fatty acid elongation / NADP binding / extracellular region
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 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	5ovl.cif.gz	364.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ovl.ent.gz	296.5 KB	Display	PDB format
PDBx/mmJSON format	5ovl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ovl_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	5ovl_full_validation.pdf.gz	1.7 MB	Display
Data in XML	5ovl_validation.xml.gz	39.2 KB	Display
Data in CIF	5ovl_validation.cif.gz	54.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ov/5ovl ftp://data.pdbj.org/pub/pdb/validation_reports/ov/5ovl	HTTPS FTP

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Related structure data

Related structure data	5ovjC 5ovkC 1uznS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ovk-d 4cql-4 6uut-d 5aij-d 4cql-1 3eh1-d 3d3w-1 1zxm-d 4i08-1 1uzn-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	#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)

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

130 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)	52.140, 69.390, 223.650
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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: 31732.795 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) / Strain (production host): pLysS References: UniProt: P71534, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 481 / 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 grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Na citrate pH 5.6, 1.0 M Li2SO4 and 0.5 M (NH4)2SO4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
Detector	Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Feb 7, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8729 Å / Relative weight: 1
Reflection	Resolution: 2.4→47.26 Å / Num. obs: 32703 / % possible obs: 99.96 % / Redundancy: 6.6 % / R_rim(I) all: 0.166 / Net I/σ(I): 10.75
Reflection shell	Resolution: 2.4→2.48 Å / R_rim(I) all: 0.52

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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: 1UZN

1uzn

Resolution: 2.4→47.256 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2194	2000	6.12 %
R_work	0.1682	-	-
obs	0.1713	32700	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.4→47.256 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6845	0	192	481	7518

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7146
X-RAY DIFFRACTION	f_angle_d	0.404	9675
X-RAY DIFFRACTION	f_dihedral_angle_d	16.753	2523
X-RAY DIFFRACTION	f_chiral_restr	0.055	1087
X-RAY DIFFRACTION	f_plane_restr	0.002	1261

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 (%)
2.4-2.46	0.3188	139	0.2274	2144	X-RAY DIFFRACTION	100
2.46-2.5265	0.2707	140	0.1985	2144	X-RAY DIFFRACTION	100
2.5265-2.6008	0.2789	142	0.1923	2175	X-RAY DIFFRACTION	100
2.6008-2.6848	0.2324	139	0.1979	2144	X-RAY DIFFRACTION	100
2.6848-2.7807	0.2198	143	0.1896	2178	X-RAY DIFFRACTION	100
2.7807-2.8921	0.2433	142	0.191	2181	X-RAY DIFFRACTION	100
2.8921-3.0237	0.2412	139	0.1773	2142	X-RAY DIFFRACTION	100
3.0237-3.183	0.2168	141	0.1789	2155	X-RAY DIFFRACTION	100
3.183-3.3824	0.2082	142	0.1741	2185	X-RAY DIFFRACTION	100
3.3824-3.6435	0.2254	144	0.1662	2214	X-RAY DIFFRACTION	100
3.6435-4.01	0.1894	144	0.1419	2198	X-RAY DIFFRACTION	100
4.01-4.5898	0.1763	143	0.1299	2212	X-RAY DIFFRACTION	100
4.5898-5.781	0.2094	148	0.1474	2267	X-RAY DIFFRACTION	100
5.781-47.2648	0.1893	154	0.153	2361	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	0.5486	-0.0248	0.1087	2.0378	-0.227	0.5136	0.0592	-0.1082	0.0378	0.1753	-0.0097	-0.001	-0.0056	0.0797	-0.0646	0.0811	-0.005	-0.0121	0.1526	-0.0217	0.1296	-14.4549	8.8389	-5.3361
2	5.96	-3.6992	4.5119	7.3843	-4.3283	4.9019	-0.2112	0.0151	0.072	0.2459	0.0249	0.4715	-0.1222	-0.3261	0.0917	0.111	-0.0151	-0.018	0.1277	-0.0145	0.128	-27.0989	5.1483	-6.0512
3	0.377	-0.1223	-0.5147	0.8445	-0.0892	0.8515	0.0108	-0.0389	0.0594	0.0689	0.0112	-0.1358	-0.0063	0.1079	-0.0096	0.1039	-0.0224	-0.0295	0.124	-0.0176	0.1498	-10.2579	3.7588	-18.0259
4	4.4718	-2.1112	-2.2181	2.9826	1.5031	2.1318	-0.1444	0.1401	-0.0023	0.1279	-0.0201	0.1093	0.3172	-0.2167	0.1548	0.2458	-0.0394	-0.0254	0.1115	-0.0001	0.114	-16.1301	-33.3721	-20.7932
5	0.3262	-0.2738	0.5079	4.6335	3.6411	4.572	0.0189	-0.0966	-0.5082	0.4791	-0.3088	0.854	0.7376	-0.2875	0.4223	0.4004	0.0033	0.0827	0.0987	0.0451	0.3831	-21.1432	-35.4101	-9.7762
6	2.343	0.0584	0.7057	5.4199	4.062	3.2199	0.2809	-0.0251	-0.3	0.4645	-0.2161	-0.2127	0.281	0.2115	0.0152	0.3034	0.0034	0.0218	0.1797	0.0134	0.0895	-13.3318	-31.0157	-2.8145
7	2.3862	-2.9576	-0.6546	5.7825	0.4584	1.2511	-0.0134	0.0234	-0.1221	0.2505	0.0103	0.3353	0.2242	-0.0574	-0.0027	0.1378	-0.0367	-0.0101	0.1561	-0.0215	0.1315	-23.2058	-13.7741	-7.7491
8	4.5373	-4.8663	-4.4496	7.6218	3.5791	6.104	-0.1398	-0.3647	0.0851	0.3322	0.1629	-0.5589	0.5063	0.3602	-0.0447	0.193	-0.0084	-0.0334	0.1379	-0.0117	0.1663	-5.4242	-23.4501	-8.4381
9	4.0902	-2.1401	0.7523	3.324	-0.5383	1.5118	-0.0202	-0.1362	0.1411	0.2173	-0.1256	0.0873	0.301	-0.0621	0.0254	0.1652	-0.0122	0.0112	0.0839	0.0138	0.048	-17.6609	-16.0634	-18.7598
10	2.5817	-1.8282	-1.5791	2.8443	0.9048	2.1681	-0.2462	0.153	0.0701	0.3006	0.112	-0.113	0.1862	0.1037	0.0411	0.1137	-0.023	-0.0242	0.0791	0.0168	0.0825	-10.6936	-13.5017	-16.2567
11	3.2699	-0.1593	1.8688	2.7163	-0.3483	3.0474	-0.2639	-0.5302	-0.014	0.1175	0.1315	0.4486	-0.0926	-0.544	0.0659	0.1463	-0.0162	0.0068	0.1597	-0.0192	0.1406	-26.7228	-18.0099	-25.1258
12	2.1312	-0.2375	-0.5238	1.0373	0.551	1.4741	-0.0585	0.2533	-0.3204	-0.0149	0.0322	0.1595	0.252	-0.0216	0.0876	0.1719	0.0161	0.0159	0.1188	0.0232	0.0704	-16.6301	-21.2392	-26.9631
13	0.8541	-0.4657	0.5175	1.8997	-0.2683	2.2848	0.0322	0.1556	-0.1486	-0.3864	-0.0472	0.0539	-0.049	-0.1992	0.0549	0.1947	0.0173	0.0022	0.1378	0.0034	0.1184	-14.6076	21.6521	-39.1615
14	0.8174	0.1928	0.6308	1.9228	1.3546	1.2616	-0.0936	0.4685	0.2694	-0.8166	0.24	-0.1723	-0.2522	0.5876	0.1554	0.5335	-0.0328	0.2026	0.2444	0.1026	0.1118	-7.891	18.2505	-52.0396
15	1.2731	0.1139	-0.1273	2.7473	-0.1888	1.4978	-0.0426	-0.1387	0.0018	-0.3811	-0.0876	0.3114	-0.0198	-0.3538	0.1813	0.0826	0.0313	-0.0079	0.1876	0.0076	0.0586	-19.5065	3.5667	-46.7712
16	7.4735	4.2974	1.9912	6.3066	3.21	4.2342	-0.5	0.306	-0.1595	-0.7323	0.2465	0.5116	-0.6522	-0.325	0.0248	0.2934	0.0154	0.0269	0.1547	0.0075	0.1292	-18.3003	-1.1212	-52.5402
17	4.924	1.391	5.5399	3.893	2.7835	6.6896	0.0108	0.6245	0.35	-0.16	0.2106	-0.457	-0.0299	0.5489	-0.2417	0.2179	0.0442	0.1148	0.2153	0.0071	0.2334	-1.7454	10.1054	-45.5611
18	1.3248	0.3949	0.0588	1.3657	0.245	1.1195	-0.1772	0.1643	-0.2408	-0.4424	0.1188	-0.3174	-0.1011	-0.1418	-0.0873	0.0695	0.0201	-0.0058	0.1311	0.0103	0.1394	-14.3842	4.5751	-37.2383
19	0.7763	0.2049	-0.2813	1.8781	0.8491	1.6108	0.0308	0.1015	-0.1099	-0.1613	-0.093	0.1112	-0.0293	-0.0956	0.0445	0.114	0.0108	-0.0023	0.107	0.0307	0.0944	-19.8683	3.8697	-35.8373
20	0.7501	0.4172	-0.4527	2.315	0.3281	1.2952	-0.0519	-0.0164	0.1398	-0.1282	0.0741	-0.0035	-0.1307	0.106	-0.0467	0.0889	-0.0023	-0.02	0.1135	0.0108	0.079	-15.6428	8.9391	-28.8756
21	0.4166	0.5511	0.0127	2.1644	-0.1826	1.0075	-0.0576	0.0679	-0.0451	-0.4113	0.058	-0.1296	0.2256	0.0582	-0.0397	0.2012	0.0423	0.0122	0.1656	-0.0183	0.1594	-12.9933	-19.7021	-48.5675
22	0.6861	-0.4303	0.2754	2.2724	-0.2614	1.8969	-0.0854	-0.0005	0.0235	-0.0827	0.0583	-0.1404	0.1537	0.1258	0.0358	0.1491	0.0149	0.0066	0.1165	-0.0055	0.073	-11.6678	-16.4649	-35.3067

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 121 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 122 through 137 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 138 through 255 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 14 through 46 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 47 through 63 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 64 through 87 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 88 through 121 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 122 through 138 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 139 through 158 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 159 through 182 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 183 through 221 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 222 through 255 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 15 through 63 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 64 through 87 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 88 through 109 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 110 through 121 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 122 through 137 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 138 through 158 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 159 through 221 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 222 through 255 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 15 through 158 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 159 through 255 )

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