PDB-8w0d: Crystal structure of Acetyl-CoA synthetase 2 from Candida albican...

ID or keywords:

Entry

Database: PDB / ID: 8w0d

Title

Crystal structure of Acetyl-CoA synthetase 2 from Candida albicans in complex with an isopropyl AMP ester inhibitor

Components

Acetyl-coenzyme A synthetase 2

Keywords

LIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Acetyl-coenzyme A synthetase 2

Function / homology

Function and homology information

acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / acetyl-CoA biosynthetic process / AMP binding / ATP binding / cytosol
Similarity search - Function

Biological species

Candida albicans (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Acetyl-CoA synthetase 2 from Candida albicans in complex with an isopropyl AMP ester inhibitor
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Feb 13, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 21, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8w0d.cif.gz	719.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8w0d.ent.gz	598.3 KB	Display	PDB format
PDBx/mmJSON format	8w0d.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/w0/8w0d ftp://data.pdbj.org/pub/pdb/validation_reports/w0/8w0d	HTTPS FTP

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Related structure data

Similar structure data	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 (6)

Deposited unit

A: Acetyl-coenzyme A synthetase 2

B: Acetyl-coenzyme A synthetase 2

C: Acetyl-coenzyme A synthetase 2

hetero molecules

229 kDa, 3 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)	139.487, 139.487, 544.117
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

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Protein , 1 types, 3 molecules ABC

#1: Protein	Acetyl-coenzyme A synthetase 2 Mass: 75908.391 Da / Num. of mol.: 3 / Mutation: V403A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Gene: ACS2 / Plasmid: CaalA.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NJN3

#1: Protein

Acetyl-coenzyme A synthetase 2

Mass: 75908.391 Da / Num. of mol.: 3 / Mutation: V403A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Candida albicans (yeast) / Gene: ACS2 / Plasmid: CaalA.00629.a.FS11 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NJN3

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Non-polymers , 6 types, 336 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-YHQ / 5'-O-{(R)-hydroxy[(propan-2-yl)oxy]phosphoryl}adenosine Mass: 389.301 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₃H₂₀N₅O₇P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.36 Å³/Da / Density % sol: 63.34 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Berkeley B12: 25% PEG 3350, 0.1M HEPES pH 7.5, 0.2M (NH4)2SO4. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1195 added to the protein prior to crystallization. plate 13752 well B12 drop 1. ...Details: Berkeley B12: 25% PEG 3350, 0.1M HEPES pH 7.5, 0.2M (NH4)2SO4. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1195 added to the protein prior to crystallization. plate 13752 well B12 drop 1. Puck: PSL-1803, Cryo: 20% Glycerol + 80% crystallant.

Crystal

Density Matthews: 3.36 Å³/Da / Density % sol: 63.34 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Berkeley B12: 25% PEG 3350, 0.1M HEPES pH 7.5, 0.2M (NH4)2SO4. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1195 added to the protein prior to crystallization. plate 13752 well B12 drop 1. ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 23, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.7→49.61 Å / Num. obs: 87265 / % possible obs: 100 % / Redundancy: 19.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.241 / R_pim(I) all: 0.055 / R_rim(I) all: 0.248 / Χ²: 1 / Net I/σ(I): 12.3 / Num. measured all: 1726771
Reflection shell	Resolution: 2.7→2.77 Å / % possible obs: 100 % / Redundancy: 20.4 % / R_merge(I) obs: 2.196 / Num. measured all: 129235 / Num. unique obs: 6323 / CC_1/2: 0.792 / R_pim(I) all: 0.496 / R_rim(I) all: 2.252 / Χ²: 1 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5233: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→49.61 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2262	4333	4.98 %
R_work	0.1841	-	-
obs	0.1861	87045	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.7→49.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14183	0	106	322	14611

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	14658
X-RAY DIFFRACTION	f_angle_d	0.632	19950
X-RAY DIFFRACTION	f_dihedral_angle_d	11.251	5278
X-RAY DIFFRACTION	f_chiral_restr	0.046	2173
X-RAY DIFFRACTION	f_plane_restr	0.005	2563

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 (%)
2.7-2.73	0.4165	149	0.3362	2709	X-RAY DIFFRACTION	100
2.73-2.76	0.3214	151	0.2862	2668	X-RAY DIFFRACTION	100
2.76-2.8	0.3373	149	0.2738	2725	X-RAY DIFFRACTION	100
2.8-2.83	0.2842	135	0.2464	2685	X-RAY DIFFRACTION	100
2.83-2.87	0.3008	137	0.2458	2692	X-RAY DIFFRACTION	100
2.87-2.91	0.2712	150	0.2303	2755	X-RAY DIFFRACTION	100
2.91-2.95	0.3023	141	0.2258	2674	X-RAY DIFFRACTION	100
2.95-2.99	0.2796	143	0.2186	2671	X-RAY DIFFRACTION	100
2.99-3.04	0.2528	159	0.222	2728	X-RAY DIFFRACTION	100
3.04-3.09	0.3185	126	0.2202	2717	X-RAY DIFFRACTION	100
3.09-3.14	0.2621	148	0.2254	2699	X-RAY DIFFRACTION	100
3.14-3.2	0.2793	145	0.2333	2722	X-RAY DIFFRACTION	100
3.2-3.26	0.2731	161	0.2249	2704	X-RAY DIFFRACTION	100
3.26-3.33	0.2558	135	0.2056	2746	X-RAY DIFFRACTION	100
3.33-3.4	0.2732	127	0.2034	2755	X-RAY DIFFRACTION	100
3.4-3.48	0.2456	158	0.1999	2698	X-RAY DIFFRACTION	100
3.48-3.57	0.2368	143	0.1913	2732	X-RAY DIFFRACTION	100
3.57-3.66	0.237	158	0.1807	2728	X-RAY DIFFRACTION	100
3.66-3.77	0.2177	150	0.1843	2745	X-RAY DIFFRACTION	100
3.77-3.89	0.2196	135	0.1763	2753	X-RAY DIFFRACTION	100
3.89-4.03	0.2345	139	0.1712	2742	X-RAY DIFFRACTION	100
4.03-4.19	0.2063	148	0.1567	2769	X-RAY DIFFRACTION	100
4.19-4.38	0.1474	128	0.1404	2792	X-RAY DIFFRACTION	100
4.38-4.62	0.1612	122	0.1295	2786	X-RAY DIFFRACTION	100
4.62-4.9	0.1735	150	0.1296	2792	X-RAY DIFFRACTION	100
4.91-5.28	0.184	145	0.1413	2803	X-RAY DIFFRACTION	100
5.28-5.81	0.2262	149	0.1672	2843	X-RAY DIFFRACTION	100
5.81-6.65	0.2042	137	0.1714	2860	X-RAY DIFFRACTION	100
6.65-8.38	0.2042	154	0.1827	2904	X-RAY DIFFRACTION	100
8.38-49.61	0.2028	161	0.1966	3115	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	0.9325	-0.137	-0.1682	0.8801	0.0329	2.3929	0.0517	0.1451	0.0391	-0.0814	0.1037	-0.1268	-0.1259	0.1307	-0.1564	0.4156	-0.064	0.0335	0.3694	0.0263	0.435	21.3396	37.1084	-21.5439
2	1.981	0.39	0.0404	3.2993	-0.2519	2.5853	0.0181	-0.0056	-0.138	-0.1606	0.0788	0.1768	0.2519	-0.35	-0.0995	0.4062	-0.0968	-0.0529	0.5421	0.057	0.3656	-3.2886	24.6686	-27.5817
3	1.4275	-0.0299	-0.3298	0.9173	0.0634	1.6251	-0.0113	0.2212	-0.0657	-0.2146	0.0725	0.013	0.2265	-0.1575	-0.0813	0.4603	-0.0796	-0.001	0.4083	0.05	0.3544	10.5578	26.6692	-31.2386
4	0.7464	-0.1659	0.1092	1.475	-0.2139	1.5743	-0.001	-0.0003	-0.1109	-0.0786	0.1053	-0.08	0.2469	0.1123	-0.104	0.4573	0.024	0.0048	0.3917	-0.0011	0.4122	22.7122	19.6428	-15.3116
5	2.3917	-2.6019	1.2519	5.6412	-4.0798	4.7028	0.0613	0.2858	-0.0624	-0.7014	-0.1104	0.1395	0.1584	0.1259	0.0752	0.7803	-0.0844	-0.0335	0.4578	-0.0435	0.5061	15.0282	-5.9949	-15.5154
6	2.8569	-0.8252	-0.0301	1.5389	-0.6033	2.3752	0.1048	-0.3742	0.4637	0.2873	0.1457	-0.1353	-0.2809	0.04	-0.2636	0.6241	0.0593	0.0478	0.4564	-0.0398	0.6326	0.3191	69.0184	25.7155
7	1.2301	-0.1154	-0.0843	2.3358	-0.5093	1.664	-0.0569	0.0063	0.0692	0.0244	0.1357	0.236	0.1781	-0.31	-0.0923	0.3716	0.023	0.0721	0.4699	0.0667	0.385	-7.3184	41.4182	7.7782
8	0.8838	0.0856	-0.0623	1.3486	-0.0882	1.3275	-0.0515	-0.1449	0.0351	0.1634	0.1163	0.0135	0.0013	-0.1582	-0.0518	0.3981	0.076	0.0711	0.5023	0.0725	0.4739	-4.211	46.6132	21.154
9	1.6657	-0.3949	0.0941	1.8716	1.9202	2.6325	0.0063	0.0667	0.1605	0.0283	-0.0301	0.3796	-0.2169	-0.4426	0.045	0.499	0.1499	0.0916	0.5758	0.1573	0.5559	-20.0963	65.7566	16.7379
10	2.2449	-2.682	-2.3415	5.4076	2.3046	5.8886	-0.5642	0.2429	-1.0345	0.6829	-0.07	0.351	0.5699	-0.502	0.6658	0.9236	0.0572	0.1536	0.8372	0.0144	0.8851	-46.4077	59.7014	20.1227
11	1.9346	-2.6278	0.2535	8.6034	-0.7312	1.536	-0.8887	0.6643	-1.3004	-0.2103	0.2308	-0.3071	1.1214	-0.4935	0.5561	1.2889	-0.0783	0.5133	0.9608	-0.3054	1.4494	-45.1938	50.723	14.6258
12	0.7644	0.0348	0.4533	0.0659	-0.3156	2.6481	0.2463	0.4821	0.5811	-0.6873	-0.2037	-0.043	-0.5207	-0.3548	0.0071	1.1103	0.2491	0.0745	0.97	0.3915	0.8218	-13.5648	78.1987	-43.7112
13	1.1435	-0.0164	-0.4593	1.1364	0.2417	1.2806	0.0614	0.1266	0.0306	-0.1338	-0.0869	0.2219	-0.1172	-0.3704	0.0236	0.4302	0.0945	-0.0477	0.7423	0.1626	0.5921	-24.5485	54.7792	-18.8855
14	1.314	-0.5825	-0.8001	3.3875	-0.1535	1.1934	0.1348	0.2159	0.1599	-0.2504	-0.0701	0.2147	-0.3536	-0.524	-0.0661	0.5515	0.1607	-0.0405	0.8279	0.1671	0.6024	-19.9992	62.1899	-29.6291
15	0.4504	-0.4303	0.055	1.7209	0.0051	0.0187	0.0062	0.3135	0.2406	-0.2189	0.0605	0.3936	-0.5141	-0.7255	-0.0248	0.7365	0.3666	0.0096	1.0424	0.2685	0.8657	-32.9403	73.3135	-29.6666
16	1.0624	-0.2919	0.3911	1.6068	0.203	0.8648	0.1094	0.5665	0.2789	-0.4583	0.0659	0.31	-0.3133	-0.3065	-0.1385	0.7868	0.2229	-0.0513	0.9686	0.2807	0.6405	-18.5455	63.5634	-45.354

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 20 through 136 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 137 through 249 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 250 through 411 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 412 through 584 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 585 through 685 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 20 through 65 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 66 through 249 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 250 through 467 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 468 through 556 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 557 through 620 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 621 through 685 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 20 through 65 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 66 through 287 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 288 through 339 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 340 through 411 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 412 through 548 )

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