PDB-7akc: Structure of the of AcylTransferase domain of phenolphthiocerol/p...

ID or keywords:

Entry

Database: PDB / ID: 7akc

Title

Structure of the of AcylTransferase domain of phenolphthiocerol/phtiocerol synthase A from Mycobacterium bovis (BCG)

Components

Phenolpthiocerol synthesis type-I polyketide synthase ppsA

Keywords

TRANSFERASE / phenolphtiocerol/phtiocerol synthase A / acyl transferase / Polyketide synthase / Mycobacterium bovis

Function / homology

Function and homology information

phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function

Biological species

Mycobacterium bovis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Brison, Y. / Nahoum, V. / Mourey, L. / Maveyraud, L.

Funding support

France, 1items

Citation

Journal: Acs Chem.Biol. / Year: 2020
Title: Molecular Basis for Extender Unit Specificity of Mycobacterial Polyketide Synthases.
Authors: Grabowska, A.D. / Brison, Y. / Maveyraud, L. / Gavalda, S. / Faille, A. / Nahoum, V. / Bon, C. / Guilhot, C. / Pedelacq, J.D. / Chalut, C. / Mourey, L.

History

Deposition	Sep 30, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 9, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 30, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 31, 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	7akc.cif.gz	122.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7akc.ent.gz	92.6 KB	Display	PDB format
PDBx/mmJSON format	7akc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7akc_validation.pdf.gz	424.3 KB	Display	wwPDB validaton report
Full document	7akc_full_validation.pdf.gz	425.7 KB	Display
Data in XML	7akc_validation.xml.gz	13.1 KB	Display
Data in CIF	7akc_validation.cif.gz	19 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ak/7akc ftp://data.pdbj.org/pub/pdb/validation_reports/ak/7akc	HTTPS FTP

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Related structure data

Related structure data	7agpC 7agqC 7agrC 7agsC 7agtC 7aguC 7ahbC 3tswS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1sd2-d 2yh6-2 4mda-d 1fsf-d 6v6n-2 5tix-1 2wnb-d 3hf6-d 6v6n-4 1sd1-d 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	#90 - Jun 2007 Fatty Acid Synthase similarity (15) #239 - Nov 2019 Phospholipase A2 similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Phenolpthiocerol synthesis type-I polyketide synthase ppsA

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, Elution volume in size exclusion chromatography is compatible with monomeric species

Unit cell

Length a, b, c (Å)	94.029, 94.029, 73.236
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

#1: Protein	Phenolpthiocerol synthesis type-I polyketide synthase ppsA Mass: 36897.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues Met609 - His617 : purification tag Residues Gly953 and Ser954 : cloning artifact Source: (gene. exp.) Mycobacterium bovis (strain BCG / Pasteur 1173P2) (bacteria) Strain: BCG / Pasteur 1173P2 / Gene: ppsA, BCG_2953 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3M7U0
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.04 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 19% (w/v) PEG 5,000 MME 0.1 M MES

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 6, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98011 Å / Relative weight: 1
Reflection	Resolution: 1.6→47.01 Å / Num. obs: 43463 / % possible obs: 98.6 % / Redundancy: 14.2 % / B_iso Wilson estimate: 30.13 Å² / CC_1/2: 1 / R_merge(I) obs: 0.04 / R_rim(I) all: 0.041 / R_sym value: 0.04 / Net I/σ(I): 31
Reflection shell	Resolution: 1.6→1.69 Å / Redundancy: 14.4 % / R_merge(I) obs: 1.092 / Mean I/σ(I) obs: 2.61 / Num. unique obs: 6973 / CC_1/2: 0.875 / R_rim(I) all: 1.134 / R_sym value: 1.092 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
BUSTER	2.10.3 (20-MAY-2020)	refinement
REFMAC	5.8.258	refinement
XDS		data scaling
XDS		data reduction
XDS		data processing
Coot		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3TSW

3tsw

Resolution: 1.6→47.01 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.933 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.103 / SU R_free Blow DPI: 0.099 / SU R_free Cruickshank DPI: 0.096

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2671	2126	4.98 %	RANDOM
R_work	0.2445	-	-	-
obs	0.2457	42725	97.6 %	-

Displacement parameters

B_iso mean: 44.55 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.0719 Å²	0 Å²	0 Å²
2-	-	-0.0719 Å²	0 Å²
3-	-	-	0.1438 Å²

Refine analyze

Luzzati coordinate error obs: 0.3 Å

Refinement step

Cycle: 1 / Resolution: 1.6→47.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1902	0	2	195	2099

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	1953	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.08	2675	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		630	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes
X-RAY DIFFRACTION	t_gen_planes		336	HARMONIC	5
X-RAY DIFFRACTION	t_it		1953	HARMONIC	10
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.22
X-RAY DIFFRACTION	t_other_torsion	15.2
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		283	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		1928	SEMIHARMONIC	4

LS refinement shell

Resolution: 1.6→1.61 Å

	R_factor	Num. reflection	% reflection
R_free	0.2763	44	5.15 %
R_work	0.2784	811	-
obs	-	-	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	6.895	-2.0415	-7.2299	4.4508	4.0903	13.8633	0.8333	-0.3854	1.478	-0.1516	0.2946	-0.1336	-0.7494	0.5464	-1.1279	0.1735	0.0285	0.2941	-0.2391	-0.0134	-0.0944	-8.6295	-19.8426	18.9305
2	5.2504	-1.1074	-3.5983	0	0.6172	3.6693	1.2235	0.2703	1.2609	-0.4801	-0.0512	-0.113	-2.0598	-1.0677	-1.1723	0.5257	0.1906	0.4894	-0.3686	0.1059	0.0281	-15.5547	-13.5754	21.5019
3	2.5708	0.3827	-1.6546	4.3303	0.1961	0	0.6671	0.299	0.7361	-0.3112	0.0312	0.0638	-1.0177	-0.4347	-0.6984	0.1465	0.129	0.1612	-0.0597	0.1062	-0.1412	-9.4835	-24.0199	12.7828
4	3.963	1.2891	-3.8487	0.1355	-2.7681	4.9793	0.9063	0.937	0.7484	0.1001	-0.0317	0.1651	-1.4734	-1.1523	-0.8745	0.2245	0.3619	0.1704	0.0893	0.2131	-0.1414	-17.39	-22.7971	13.5812
5	3.5916	-1.4745	-6.9623	4.6219	-6.0478	26.8551	1.1105	1.0042	0.7042	0.1307	-0.2083	0.1609	-1.8109	-2.1873	-0.9022	0.0491	0.3791	0.1186	0.173	0.1854	-0.0652	-25.9831	-23.8153	22.5788
6	2.0706	0.8186	-0.2018	2.5572	-0.0521	1.917	0.1239	-0.4452	0.6553	0.019	0.1772	-0.2037	-0.1527	0.2382	-0.3011	-0.0282	0.0665	0.0089	-0.0016	-0.0098	-0.1523	-7.115	-35.3686	32.1932
7	11.2505	0.8159	-4.8712	1.9616	-0.9572	6.6666	-0.073	-0.2653	-0.3416	-0.0768	0.0204	-0.0726	0.3254	0.1649	0.0525	0.0033	0.0858	-0.0132	-0.031	0.0134	-0.1516	-8.0434	-45.7151	30.8217
8	3.9552	1.609	-2.4633	1.974	-2.8037	4.1093	0.0786	-0.0379	0.1055	-0.0242	0.0167	0.013	0.0471	0.0587	-0.0953	0.0077	0.0473	0.0083	-0.0233	-0.0024	-0.1338	-8.7822	-37.648	26.0037
9	7.6787	0.1867	-4.7386	2.1548	-1.7852	6.9897	0.1379	-0.1101	0.2643	0.0648	0.0116	-0.0756	-0.1551	0.2125	-0.1495	-0.0114	0.0623	0.0037	0.007	-0.026	-0.144	-7.3487	-36.1965	29.8969
10	4.3007	0.2399	1.7575	1.3626	0.6351	5.053	-0.0111	-0.3522	-0.0831	0.2389	0.2974	0.0403	0.1997	0.3182	-0.2863	-0.0272	0.0886	-0.0113	0.0398	-0.043	-0.1719	-6.7654	-39.5025	40.037
11	17.8239	-11.9612	0.7552	18.1637	0.9395	6.7172	-0.7341	-0.6248	1.281	1.2304	0.4868	-0.2631	-0.3503	0.4302	0.2473	-0.1119	0.0035	0.0174	0.0326	-0.1344	-0.1657	-3.4424	-32.9294	36.2901
12	4.3225	0.1458	-1.8604	0.4461	0.614	1.7014	0.047	-0.12	0.2672	-0.3394	0.2105	0.2331	-0.2383	-0.2143	-0.2575	-0.0064	0.0416	0.0269	-0.0018	0.0205	-0.0973	-17.9187	-31.7913	29.8354
13	8.537	-4.3663	-5.1882	4.6968	-3.3435	5.8074	0.4959	1.1614	-0.3939	-0.1335	-0.327	0.5255	0.118	-1.4158	-0.1689	-0.1168	0.1183	-0.0442	0.2828	-0.0235	-0.1234	-28.8624	-34.1315	22.3184
14	23.2635	2.1605	-3.1024	15.8817	0.7987	10.6372	-0.404	0.5146	-0.5044	-1.3447	0.0148	0.4029	0.0139	-2.5162	0.3892	-0.0534	0.7536	-0.0467	0.7298	0.3573	-0.602	-25.5132	-25.2362	6.8067
15	4.9989	1.4973	-4.2264	10.2003	0.3452	2.5066	0.2592	1.1821	-0.0599	-1.0687	-0.105	0.0485	0.0808	-0.9013	-0.1542	0.0484	0.1071	-0.0035	0.1793	0.0533	-0.2288	-12.6286	-33.2775	10.0564
16	4.1317	-0.3644	-2.7832	2.7478	-3.7622	11.6779	0.2287	1.0056	-0.0576	-0.0783	0.0592	0.3042	-0.0177	-1.7425	-0.2879	-0.0812	0.1208	-0.0217	0.3093	0.0403	-0.2129	-21.5612	-33.075	15.3567
17	3.5334	0.4311	-3.734	0	0.3786	6.0581	0.0123	-0.029	0.1817	-0.1803	0.2128	0.0186	-0.0981	0.1274	-0.2251	0.034	0.0224	0.0486	-0.0229	0.0098	-0.1392	-5.1671	-32.9433	14.5454
18	6.0562	-3.4099	-7.4948	13.7593	14.2272	20.1159	0.6723	0.1512	0.9173	0.1886	0.2965	0.3268	-0.8368	0.1537	-0.9687	0.1248	-0.0233	0.2875	-0.2354	0.0121	-0.0735	-2.9111	-22.049	13.1311
19	18.058	-2.0849	-8.7388	10.5098	1.7871	12.9524	0.2104	-0.6428	0.7426	0.1242	0.2072	-0.5898	-0.5501	0.962	-0.4176	-0.0107	-0.1184	0.0646	-0.037	-0.0524	-0.2244	2.4914	-28.0294	19.0475
20	13.0383	1.7851	-10.8214	0.7802	-0.3546	8.8493	0.53	-0.5721	0.8344	1.2225	-0.0473	-0.1339	-0.0225	0.9115	-0.4826	0.1643	-0.2808	0.3758	-0.258	-0.2689	-0.135	1.8124	-19.0885	17.3938

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|629 - A\|642 }
2	X-RAY DIFFRACTION	2	{ A\|682 - A\|712 }
3	X-RAY DIFFRACTION	3	{ A\|713 - A\|720 }
4	X-RAY DIFFRACTION	4	{ A\|721 - A\|732 }
5	X-RAY DIFFRACTION	5	{ A\|733 - A\|754 }
6	X-RAY DIFFRACTION	6	{ A\|755 - A\|764 }
7	X-RAY DIFFRACTION	7	{ A\|765 - A\|776 }
8	X-RAY DIFFRACTION	8	{ A\|777 - A\|786 }
9	X-RAY DIFFRACTION	9	{ A\|787 - A\|794 }
10	X-RAY DIFFRACTION	10	{ A\|795 - A\|809 }
11	X-RAY DIFFRACTION	11	{ A\|810 - A\|816 }
12	X-RAY DIFFRACTION	12	{ A\|817 - A\|824 }
13	X-RAY DIFFRACTION	13	{ A\|825 - A\|837 }
14	X-RAY DIFFRACTION	14	{ A\|838 - A\|846 }
15	X-RAY DIFFRACTION	15	{ A\|847 - A\|859 }
16	X-RAY DIFFRACTION	16	{ A\|860 - A\|874 }
17	X-RAY DIFFRACTION	17	{ A\|875 - A\|888 }
18	X-RAY DIFFRACTION	18	{ A\|889 - A\|902 }
19	X-RAY DIFFRACTION	19	{ A\|903 - A\|918 }
20	X-RAY DIFFRACTION	20	{ A\|919 - A\|930 }

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