PDB-5ey9: Structure of FadD32 from Mycobacterium marinum complexed to AMPC12

ID or keywords:

Entry

Database: PDB / ID: 5ey9

Title

Structure of FadD32 from Mycobacterium marinum complexed to AMPC12

Components

Long-chain-fatty-acid--AMP ligase FadD32

Keywords

LIGASE / fatty-acyl AMP ligase

Function / homology

Function and homology information

long-chain-fatty-acid-[acyl-carrier-protein] ligase / long-chain fatty acid [acyl-carrier-protein] ligase activity / adenylyltransferase activity / fatty acid biosynthetic process / ATP binding / plasma membrane
Similarity search - Function

Biological species

Mycobacterium marinum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Guillet, V. / Maveyraud, L. / Mourey, L.

Funding support

1items

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: Insight into Structure-Function Relationships and Inhibition of the Fatty Acyl-AMP Ligase (FadD32) Orthologs from Mycobacteria.
Authors: Guillet, V. / Galandrin, S. / Maveyraud, L. / Ladeveze, S. / Mariaule, V. / Bon, C. / Eynard, N. / Daffe, M. / Marrakchi, H. / Mourey, L.

History

Deposition	Nov 24, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 23, 2016	Group: Database references
Revision 1.2	Apr 20, 2016	Group: Database references
Revision 1.3	Jan 10, 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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PDBx/mmCIF format	5ey9.cif.gz	487 KB	Display	PDBx/mmCIF format
PDB format	pdb5ey9.ent.gz	398 KB	Display	PDB format
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Validation report

Summary document	5ey9_validation.pdf.gz	842.4 KB	Display	wwPDB validaton report
Full document	5ey9_full_validation.pdf.gz	850.2 KB	Display
Data in XML	5ey9_validation.xml.gz	47.8 KB	Display
Data in CIF	5ey9_validation.cif.gz	68.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ey/5ey9 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/5ey9	HTTPS FTP

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Related structure data

Related structure data	5ey8C 3kxwS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4c5c-d 3pmw-1 3zts-1 5ey8-5 4iy5-d 5o9a-1 3w7f-d 4c5a-d 1wvj-1 4c5b-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#78 - Jun 2006 Luciferase similarity (2)

Deposited unit

A: Long-chain-fatty-acid--AMP ligase FadD32

B: Long-chain-fatty-acid--AMP ligase FadD32

hetero molecules

140 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Long-chain-fatty-acid--AMP ligase FadD32

hetero molecules

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

2

B: Long-chain-fatty-acid--AMP ligase FadD32

hetero molecules

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

Unit cell

Length a, b, c (Å)	71.790, 100.150, 212.320
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Long-chain-fatty-acid--AMP ligase FadD32 / FAAL / Acyl-AMP synthetase Mass: 68971.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum (bacteria) / Gene: fadD32, MMAR_5365 / Production host: Escherichia coli (E. coli) References: UniProt: B2HMK0, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Chemical	ChemComp-5SV / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate Mass: 627.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₃₀H₅₄N₅O₇P
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.81 Å³/Da / Density % sol: 56.27 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.7 / Details: PEG 6000 28% TrisHCl 100 mM / PH range: 8.7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9334 Å / Relative weight: 1
Reflection	Resolution: 2.5→48.7 Å / Num. all: 53766 / Num. obs: 53766 / % possible obs: 99.8 % / Redundancy: 4.8 % / R_sym value: 0.148 / Net I/σ(I): 7.7
Reflection shell	Resolution: 2.5→2.64 Å / Redundancy: 5 % / R_merge(I) obs: 0.484 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
BALBES		phasing
SCALA		data scaling
MOSFLM		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KXW

3kxw

Resolution: 2.5→48.7 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 22.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2382	2722	5.08 %	random
R_work	0.1847	-	-	-
obs	0.1875	53585	99.55 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→48.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9369	0	112	538	10019

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	9710
X-RAY DIFFRACTION	f_angle_d	0.786	13218
X-RAY DIFFRACTION	f_dihedral_angle_d	13.221	3513
X-RAY DIFFRACTION	f_chiral_restr	0.03	1470
X-RAY DIFFRACTION	f_plane_restr	0.004	1756

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 (%)
2.5-2.5455	0.3069	157	0.2335	2586	X-RAY DIFFRACTION	100
2.5455-2.5944	0.2934	136	0.2269	2662	X-RAY DIFFRACTION	100
2.5944-2.6474	0.2969	146	0.2271	2659	X-RAY DIFFRACTION	100
2.6474-2.7049	0.2965	157	0.2369	2619	X-RAY DIFFRACTION	100
2.7049-2.7678	0.3082	138	0.2213	2666	X-RAY DIFFRACTION	100
2.7678-2.8371	0.2745	137	0.2159	2640	X-RAY DIFFRACTION	100
2.8371-2.9138	0.2863	142	0.2175	2655	X-RAY DIFFRACTION	100
2.9138-2.9995	0.2783	141	0.2188	2689	X-RAY DIFFRACTION	100
2.9995-3.0963	0.3161	145	0.217	2642	X-RAY DIFFRACTION	100
3.0963-3.2069	0.2693	141	0.212	2649	X-RAY DIFFRACTION	100
3.2069-3.3353	0.2598	143	0.1932	2666	X-RAY DIFFRACTION	100
3.3353-3.4871	0.2445	144	0.1897	2663	X-RAY DIFFRACTION	100
3.4871-3.6708	0.2286	141	0.1824	2701	X-RAY DIFFRACTION	100
3.6708-3.9007	0.2091	136	0.1666	2676	X-RAY DIFFRACTION	100
3.9007-4.2018	0.2018	153	0.1559	2707	X-RAY DIFFRACTION	100
4.2018-4.6243	0.1921	146	0.1496	2692	X-RAY DIFFRACTION	100
4.6243-5.2928	0.1886	148	0.1488	2720	X-RAY DIFFRACTION	100
5.2928-6.6656	0.2297	138	0.1678	2762	X-RAY DIFFRACTION	99
6.6656-48.7471	0.1792	133	0.164	2809	X-RAY DIFFRACTION	96

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	2.1571	-0.7368	-0.1097	2.8148	0.6201	2.4301	0.016	-0.135	-0.3449	-0.1062	-0.0812	0.2969	-0.0513	-0.4665	0.053	0.1941	-0.0255	0.018	0.3348	0.0354	0.3416	-11.485	-2.0649	23.2227
2	1.721	0.0917	-0.7924	2.6125	-0.3091	2.8414	0.0644	-0.0738	0.1335	-0.1579	-0.0806	-0.0726	-0.3555	-0.0398	-0.0149	0.3469	0.0572	-0.0609	0.2625	-0.0567	0.2674	-4.668	14.8407	21.931
3	2.0455	-0.5563	-0.872	2.1591	0.3844	2.6451	-0.0477	-0.0563	0.3713	-0.0973	0.0243	0.0089	-0.4413	-0.1782	-0.0223	0.3837	0.0614	-0.0655	0.2739	-0.0331	0.3494	-4.1441	19.0923	20.0684
4	0.9032	0.045	0.2232	1.1291	-0.4005	2.9212	-0.0524	-0.1272	-0.0946	0.1456	0.0064	0.08	0.0972	-0.11	0.0021	0.2617	0.0131	-0.0162	0.2408	-0.0099	0.2561	3.9625	-6.9797	27.0317
5	1.28	-0.4522	0.1643	1.3332	-0.1375	2.7809	0.0935	0.0626	-0.1427	-0.1869	-0.0325	-0.1203	0.2286	0.1417	0.0044	0.2527	-0.0012	-0.009	0.2036	-0.0376	0.232	10.4859	-10.5379	3.4998
6	2.0972	-0.011	0.7159	1.0382	-0.1378	0.2502	0.0254	0.3269	0.3415	-0.11	-0.1029	-0.1395	0.0175	0.164	0.0269	0.2906	-0.0025	0.0431	0.5114	0.0852	0.285	32.1168	-1.164	15.0476
7	2.6954	-0.4247	0.7929	1.3035	-0.396	0.4093	-0.1361	0.3937	0.8012	0.0132	0.05	-0.3063	-0.1526	0.1808	0.0357	0.2143	-0.0256	-0.0038	0.4635	0.0587	0.408	30.8148	2.1052	19.6342
8	1.5597	-0.7319	-0.6904	2.6962	0.4034	1.2067	0.0452	0.1591	-0.4157	-0.2027	-0.052	0.4801	0.0194	-0.2328	-0.0267	0.2825	-0.0453	-0.0181	0.2525	-0.0169	0.3895	25.0241	52.7986	43.5702
9	1.5613	0.0955	-0.825	1.9299	-0.0784	2.0248	0.1344	-0.024	-0.0089	-0.1807	-0.0742	-0.0429	-0.2314	0.0373	-0.1041	0.3533	0.0111	0.012	0.1844	-0.0293	0.2466	34.0647	68.5857	42.5502
10	2.4656	0.0074	-0.1194	1.7429	0.2675	2.2559	-0.0273	0.0164	0.2422	-0.0566	0.0964	-0.0088	-0.2214	-0.0118	-0.0758	0.3551	0.0317	0.0472	0.1918	0.0146	0.2627	35.0235	72.9498	40.1266
11	0.0828	-0.155	-0.1431	1.1944	-0.6991	1.6023	-0.0066	-0.0342	-0.0252	0.0292	0.0517	-0.0074	-0.0211	-0.0075	-0.0346	0.1841	-0.005	0.0075	0.1963	-0.0013	0.2131	39.9341	45.7422	47.1911
12	0.567	-0.8294	-0.1843	1.9098	-0.2128	2.0634	0.1291	0.0447	-0.0015	-0.1575	-0.0196	-0.0809	0.1579	0.1556	-0.1061	0.2523	0.0026	-0.0029	0.2143	-0.0257	0.2057	45.6066	41.8766	23.5614
13	1.8029	-0.5022	0.9609	1.5159	0.7563	1.2958	0.103	0.0003	0.3212	0.0162	-0.0186	-0.444	-0.0852	0.3236	-0.0972	0.3047	-0.0556	0.0178	0.4308	0.011	0.3969	68.8392	48.122	35.1734
14	2.4688	-0.4651	-0.3211	1.8906	0.3223	0.8356	0.0074	-0.0896	0.499	-0.0797	0.1691	-0.3902	-0.0937	0.3106	-0.1683	0.2047	-0.0703	0.0132	0.3232	-0.0217	0.3211	67.7576	51.1224	39.8023

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 49 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 134 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 135 through 194 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 195 through 353 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 354 through 475 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 476 through 562 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 563 through 625 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 3 through 49 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 50 through 134 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 135 through 194 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 195 through 353 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 354 through 475 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 476 through 562 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 563 through 625 )

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