PDB-5icr: 2.25 Angstrom Resolution Crystal Structure of Fatty-Acid-CoA Liga...

ID or keywords:

Entry

Database: PDB / ID: 5icr

Title

2.25 Angstrom Resolution Crystal Structure of Fatty-Acid-CoA Ligase (FadD32) from Mycobacterium smegmatis in complex with Inhibitor 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine.

Components

Acyl-CoA synthase

Keywords

LIGASE/LIGASE INHIBITOR / Fatty-Acid-CoA Ligase / FadD32 / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / LIGASE-LIGASE INHIBITOR complex

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 / cytosol
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Minasov, G. / Shuvalova, L. / Hung, D. / Fisher, S.L. / Edelstein, J. / Kiryukhina, O. / Dubrovska, I. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 2.25 Angstrom Resolution Crystal Structure of Fatty-Acid-CoA Ligase (FadD32) from Mycobacterium smegmatis in complex with Inhibitor 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine.
Authors: Minasov, G. / Shuvalova, L. / Hung, D. / Fisher, S.L. / Edelstein, J. / Kiryukhina, O. / Dubrovska, I. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Feb 23, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 6, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5icr.cif.gz	970.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5icr.ent.gz	810.9 KB	Display	PDB format
PDBx/mmJSON format	5icr.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/ic/5icr ftp://data.pdbj.org/pub/pdb/validation_reports/ic/5icr	HTTPS FTP

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Related structure data

Related structure data	5hm3S S: Starting model for refinement
Similar structure data	1lla-d 3kfm-1 1nol-d 5ejd-6 4r0m-1 1ll1-d 3uoz-1 5ns9-d 3rt6-1 3mey-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) 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
Other databases	TargetTrack: CSGID-idp95303

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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: Acyl-CoA synthase

B: Acyl-CoA synthase

C: Acyl-CoA synthase

D: Acyl-CoA synthase

hetero molecules

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

1

A: Acyl-CoA synthase

hetero molecules

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

2

B: Acyl-CoA synthase

hetero molecules

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

3

C: Acyl-CoA synthase

hetero molecules

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

4

D: Acyl-CoA synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.294, 153.561, 201.253
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Acyl-CoA synthase / Fatty-acid-CoA ligase FadD32 Mass: 70477.852 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: fadD32, MSMEG_6393, MSMEI_6225 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Star (DE3) / References: UniProt: A0R618

#1: Protein

Acyl-CoA synthase / Fatty-acid-CoA ligase FadD32

Mass: 70477.852 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: fadD32, MSMEG_6393, MSMEI_6225 / Plasmid: pET28a / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Star (DE3) / References: UniProt: A0R618

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Non-polymers , 5 types, 1136 molecules

#2: Chemical	ChemComp-649 / 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine Mass: 606.691 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₈N₆O₈S
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1125 / 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: 2.46 Å³/Da / Density % sol: 50.1 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 15.2mg/ml, 0.01M Tris-HCL buffer pH(8.3), 0.5mM TCEP; Screen: PACT (G6), 0.2M Sodium formate, 0.1M Bis-Tris propane pH 7.5, 20%(w/v) PEG 3350.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2015 / Details: C(111)
Radiation	Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.25→30 Å / Num. obs: 133115 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / B_iso Wilson estimate: 42.6 Å² / CC_1/2: 0.842 / R_merge(I) obs: 0.081 / R_sym value: 0.081 / Net I/σ(I): 24.1
Reflection shell	Resolution: 2.25→2.29 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.699 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HM3

5hm3

Resolution: 2.25→29.86 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.942 / SU B: 11.548 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.201 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21907	6648	5 %	RANDOM
R_work	0.17263	-	-	-
obs	0.17494	126351	99.92 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 48.823 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.08 Å²	0 Å²	0 Å²
2-	-	2.47 Å²	0 Å²
3-	-	-	-1.39 Å²

Refinement step

Cycle: 1 / Resolution: 2.25→29.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18704	0	200	1125	20029

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	19635
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	18442
X-RAY DIFFRACTION	r_angle_refined_deg	1.554	1.962	26794
X-RAY DIFFRACTION	r_angle_other_deg	0.926	3	42367
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.44	5	2479
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.597	23.244	894
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.76	15	2958
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.254	15	177
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	2963
X-RAY DIFFRACTION	r_gen_planes_refined	0.022	0.021	22560
X-RAY DIFFRACTION	r_gen_planes_other	0.018	0.02	4547
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.834	2.97	9889
X-RAY DIFFRACTION	r_mcbond_other	1.834	2.97	9888
X-RAY DIFFRACTION	r_mcangle_it	3.121	4.436	12377
X-RAY DIFFRACTION	r_mcangle_other	3.121	4.437	12378
X-RAY DIFFRACTION	r_scbond_it	2.075	3.248	9746
X-RAY DIFFRACTION	r_scbond_other	2.075	3.248	9746
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.281	4.765	14418
X-RAY DIFFRACTION	r_long_range_B_refined	6.517	24.392	22498
X-RAY DIFFRACTION	r_long_range_B_other	6.358	24.08	22076
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.317	466	-
R_work	0.277	9214	-
obs	-	-	99.98 %

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	1.6737	0.0804	0.1022	2.2151	0.8452	1.2452	0.0489	-0.0615	0.3993	-0.0674	0.0063	0.0841	-0.4383	0.1384	-0.0552	0.292	-0.0552	-0.0185	0.1242	-0.0183	0.2276	37.6312	85.6139	36.2173
2	1.1943	-0.1031	-0.0046	1.5674	-0.3664	1.344	0.0475	-0.168	0.1831	0.1021	0.0024	-0.1415	-0.1547	0.2305	-0.05	0.0812	-0.0512	-0.0171	0.1418	-0.0329	0.053	48.7923	70.9028	40.4681
3	0.7995	0.0564	-0.1196	0.9533	0.0505	1.4727	0.0099	0.1105	0.161	-0.1163	-0.0468	0.173	-0.1047	-0.2187	0.0368	0.1009	0.0214	-0.0292	0.0594	0.0087	0.063	27.5207	73.1655	22.3579
4	2.2506	-0.1405	0.6473	1.2609	0.1428	4.545	-0.012	0.0864	-0.1875	-0.1518	-0.0542	0.1492	0.2831	-0.4198	0.0662	0.1086	-0.041	-0.0266	0.0553	-0.0225	0.0439	21.6838	48.4901	19.5538
5	1.4804	-0.8098	0.7001	1.9089	-0.0606	3.4819	0.0184	-0.1385	-0.1696	-0.0106	-0.0024	0.1853	0.2916	-0.4026	-0.0161	0.0588	-0.0557	0.0093	0.0689	0.0008	0.0276	21.3072	48.5894	27.6892
6	2.5856	0.1732	-0.2004	1.5593	0.7534	1.8632	-0.1797	-0.3236	0.6624	-0.0788	0.2179	0.017	-0.2916	-0.0249	-0.0383	0.1312	0.0093	-0.0377	0.1613	-0.0988	0.173	78.4369	78.045	86.3155
7	3.3076	-0.6639	-1.0556	1.0104	0.1537	2.3423	-0.3452	-0.4683	0.1538	0.0997	0.2871	-0.0474	0.1683	0.2898	0.0581	0.0827	0.0139	0.007	0.1947	-0.0559	0.0339	89.0967	67.4026	87.8513
8	1.8477	0.3236	0.8738	0.6208	0.3752	1.0182	-0.1372	0.1957	0.1479	-0.0518	0.0756	0.1589	-0.1577	-0.1249	0.0616	0.0687	-0.0202	-0.0206	0.2251	0.0185	0.0901	67.0899	65.4676	69.1607
9	4.273	-0.6909	0.0133	1.3261	-0.3872	3.5742	0.0722	0.3391	-0.9117	0.1167	-0.0195	0.31	0.224	-0.074	-0.0527	0.0419	0.0041	-0.0224	0.0888	-0.1088	0.3336	71.1291	38.9512	67.3483
10	2.906	-0.6866	0.434	2.2732	0.8894	1.7461	0.0372	-0.0329	-0.8256	0.5135	0.1835	0.046	0.3563	-0.2165	-0.2208	0.1717	-0.03	-0.0184	0.2045	0.0385	0.4006	69.6561	40.2863	75.3109
11	1.4588	0.0395	0.0971	2.1589	0.089	1.8063	-0.1064	-0.3957	-0.4658	0.2866	0.017	0.2362	0.1397	-0.1514	0.0894	0.1084	-0.0073	0.0676	0.2132	0.182	0.2245	99.9985	30.6323	90.5961
12	1.8795	0.4683	0.0523	1.2617	0.0389	1.53	-0.0395	-0.2928	-0.5201	0.174	-0.0177	-0.0632	0.2484	0.1544	0.0572	0.0727	0.0385	0.0276	0.1276	0.1243	0.1735	112.7583	33.0209	82.6882
13	1.3578	0.3852	-0.462	1.0562	-0.203	1.162	-0.0724	0.0918	-0.3943	-0.1451	0.0059	-0.0347	0.1975	0.1038	0.0665	0.0625	0.021	0.0223	0.1024	-0.0286	0.1547	114.6552	38.632	63.889
14	3.0065	-0.3275	-0.4191	3.6463	-0.8127	2.5552	-0.0285	-0.0893	0.2681	0.0538	0.0441	-0.0109	-0.2293	0.1641	-0.0156	0.0272	-0.0238	-0.0013	0.0371	-0.0124	0.0268	111.504	64.4086	66.9981
15	1.7795	-0.8728	0.1642	1.7208	-0.3158	1.5594	-0.1689	-0.3162	0.057	0.2192	0.1498	-0.1249	-0.198	0.1643	0.019	0.1138	-0.0228	-0.0018	0.1788	-0.0705	0.0469	112.5087	62.4107	75.0179
16	1.1477	-0.9578	-0.7222	2.5816	-0.4878	1.286	-0.2063	-0.1394	-0.1422	-0.0145	0.1077	-0.0449	0.3423	-0.0394	0.0985	0.279	-0.0001	0.0449	0.1555	0.0723	0.1903	49.0719	22.163	38.0901
17	1.1067	-1.3605	-0.7268	2.7219	1.1233	2.7528	-0.0674	-0.16	-0.1096	0.0905	0.1348	0.0426	0.2032	-0.1492	-0.0674	0.0553	-0.0155	0.0383	0.1031	0.0301	0.067	42.5774	36.0144	39.8305
18	1.0502	-0.3232	-0.1302	1.4011	-0.282	1.9201	-0.0191	0.1383	-0.1705	-0.187	-0.1745	-0.4829	0.334	0.3739	0.1937	0.1703	0.1183	0.138	0.1355	0.0475	0.293	63.1231	30.0708	20.3815
19	2.2228	-0.1303	-0.3298	2.8363	0.2688	5.1451	0.0573	0.3554	0.0841	-0.2264	-0.179	-0.6222	-0.2175	0.5181	0.1217	0.0577	0.0039	0.1038	0.1427	0.0785	0.2588	68.4178	55.1105	17.5035
20	2.0884	-0.6454	0.438	3.2352	-0.1964	3.3389	0.0233	0.0871	0.0438	0.1394	-0.151	-0.6921	-0.2872	0.6468	0.1277	0.0442	-0.0504	-0.009	0.1713	0.0535	0.2735	70.1634	54.7872	25.9002

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 52
2	X-RAY DIFFRACTION	2	A	53 - 193
3	X-RAY DIFFRACTION	3	A	194 - 482
4	X-RAY DIFFRACTION	4	A	483 - 556
5	X-RAY DIFFRACTION	5	A	557 - 630
6	X-RAY DIFFRACTION	6	B	8 - 111
7	X-RAY DIFFRACTION	7	B	112 - 194
8	X-RAY DIFFRACTION	8	B	195 - 482
9	X-RAY DIFFRACTION	9	B	483 - 556
10	X-RAY DIFFRACTION	10	B	557 - 629
11	X-RAY DIFFRACTION	11	C	7 - 166
12	X-RAY DIFFRACTION	12	C	167 - 298
13	X-RAY DIFFRACTION	13	C	299 - 482
14	X-RAY DIFFRACTION	14	C	483 - 557
15	X-RAY DIFFRACTION	15	C	558 - 630
16	X-RAY DIFFRACTION	16	D	7 - 109
17	X-RAY DIFFRACTION	17	D	110 - 194
18	X-RAY DIFFRACTION	18	D	195 - 482
19	X-RAY DIFFRACTION	19	D	483 - 555
20	X-RAY DIFFRACTION	20	D	556 - 629

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 1136 molecules

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