PDB-8w0j: Crystal structure of Acetyl-CoA synthetase 2 from Candida albican...

ID or keywords:

Entry

Database: PDB / ID: 8w0j

Title

Crystal structure of Acetyl-CoA synthetase 2 from Candida albicans in complex with a propyne 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: 2.85 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 a propyne 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	8w0j.cif.gz	704.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8w0j.ent.gz	587.3 KB	Display	PDB format
PDBx/mmJSON format	8w0j.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/w0/8w0j ftp://data.pdbj.org/pub/pdb/validation_reports/w0/8w0j	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

231 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)	139.073, 139.073, 544.504
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, 206 molecules

#2: Chemical	ChemComp-YHT / 5'-O-{(S)-hydroxy[(prop-2-yn-1-yl)oxy]phosphoryl}adenosine Mass: 385.269 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₃H₁₆N₅O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 177 / 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: 3.34 Å³/Da / Density % sol: 63.15 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Berkeley B5: 200 mM Lithium sulfate 20% (w/v) PEG 3350. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1196 added to the protein prior to crystallization. plate 13579 well B5 drop 2. Puck: ...Details: Berkeley B5: 200 mM Lithium sulfate 20% (w/v) PEG 3350. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1196 added to the protein prior to crystallization. plate 13579 well B5 drop 2. Puck: PSL-1111, Cryo: 20% PEG 200 + 80% crystallant.

Crystal

Density Matthews: 3.34 Å³/Da / Density % sol: 63.15 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Berkeley B5: 200 mM Lithium sulfate 20% (w/v) PEG 3350. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1196 added to the protein prior to crystallization. plate 13579 well B5 drop 2. Puck: ...

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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: 0.9785 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 9, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 2.85→49.62 Å / Num. obs: 74076 / % possible obs: 100 % / Redundancy: 11.1 % / CC_1/2: 0.996 / R_merge(I) obs: 0.219 / R_pim(I) all: 0.068 / R_rim(I) all: 0.23 / Χ²: 1 / Net I/σ(I): 9.8 / Num. measured all: 819599
Reflection shell	Resolution: 2.85→2.91 Å / % possible obs: 100 % / Redundancy: 11.7 % / R_merge(I) obs: 1.839 / Num. measured all: 52402 / Num. unique obs: 4495 / CC_1/2: 0.745 / R_pim(I) all: 0.556 / R_rim(I) all: 1.922 / Χ²: 0.99 / 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: 2.85→49.62 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2263	3674	4.97 %
R_work	0.1958	-	-
obs	0.1973	73907	99.93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.85→49.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13829	0	223	177	14229

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	14417
X-RAY DIFFRACTION	f_angle_d	0.581	19608
X-RAY DIFFRACTION	f_dihedral_angle_d	11.098	5188
X-RAY DIFFRACTION	f_chiral_restr	0.044	2116
X-RAY DIFFRACTION	f_plane_restr	0.004	2503

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 (%)
2.85-2.89	0.3106	163	0.3007	2622	X-RAY DIFFRACTION	100
2.89-2.93	0.3246	123	0.2856	2649	X-RAY DIFFRACTION	100
2.93-2.97	0.3383	121	0.2829	2685	X-RAY DIFFRACTION	100
2.97-3.01	0.2765	133	0.2775	2640	X-RAY DIFFRACTION	100
3.01-3.06	0.3344	130	0.2652	2636	X-RAY DIFFRACTION	100
3.06-3.11	0.2815	151	0.2614	2632	X-RAY DIFFRACTION	100
3.11-3.16	0.3323	148	0.2649	2692	X-RAY DIFFRACTION	100
3.16-3.22	0.2956	135	0.2613	2636	X-RAY DIFFRACTION	100
3.22-3.28	0.2767	143	0.2461	2632	X-RAY DIFFRACTION	100
3.28-3.35	0.2894	164	0.2309	2652	X-RAY DIFFRACTION	100
3.35-3.42	0.2783	137	0.2239	2642	X-RAY DIFFRACTION	100
3.42-3.5	0.2824	154	0.2175	2674	X-RAY DIFFRACTION	100
3.5-3.59	0.2104	133	0.2043	2673	X-RAY DIFFRACTION	100
3.59-3.69	0.2528	137	0.2031	2664	X-RAY DIFFRACTION	100
3.69-3.8	0.2529	133	0.1993	2696	X-RAY DIFFRACTION	100
3.8-3.92	0.1996	138	0.1875	2690	X-RAY DIFFRACTION	100
3.92-4.06	0.2162	131	0.1771	2679	X-RAY DIFFRACTION	100
4.06-4.22	0.1558	150	0.1605	2716	X-RAY DIFFRACTION	100
4.22-4.41	0.1588	162	0.1481	2659	X-RAY DIFFRACTION	100
4.41-4.65	0.1496	125	0.1398	2757	X-RAY DIFFRACTION	100
4.65-4.94	0.1908	129	0.1406	2726	X-RAY DIFFRACTION	100
4.94-5.32	0.1989	139	0.1531	2747	X-RAY DIFFRACTION	100
5.32-5.85	0.2055	131	0.1721	2773	X-RAY DIFFRACTION	100
5.85-6.7	0.2274	149	0.1896	2794	X-RAY DIFFRACTION	100
6.7-8.43	0.1998	159	0.1982	2815	X-RAY DIFFRACTION	100
8.43-49.62	0.2209	156	0.1961	3052	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	1.1026	-0.0987	-0.3435	1.3822	0.0836	2.299	-0.0038	0.1202	0.1067	-0.1256	0.1713	-0.1255	-0.14	0.2508	-0.1741	0.4479	-0.0838	0.0264	0.4216	0.0143	0.4274	21.2269	36.7971	-21.8381
2	2.1501	0.3897	0.2562	1.5853	0.227	2.5625	0.0303	0.1972	-0.0888	-0.178	0.0751	0.135	0.2719	-0.3988	-0.113	0.4643	-0.1105	-0.0283	0.4579	0.081	0.3687	-2.435	26.0548	-26.7674
3	1.4248	-0.2263	-0.4553	0.9662	-0.0798	3.4734	-0.0758	0.0991	-0.0754	-0.1579	0.142	-0.0715	0.4121	0.0394	-0.0577	0.4531	-0.0525	0.0332	0.3046	0.0087	0.3859	22.3086	23.3626	-23.4815
4	3.4419	-3.0955	1.4567	7.3559	-6.1425	6.2919	-0.0351	0.1767	-0.3663	-0.2685	0.1971	0.3439	0.0929	-0.1225	-0.1232	0.7447	-0.1036	0.0355	0.4019	-0.0732	0.4946	13.6539	-4.6489	-15.3377
5	1.6378	-0.5924	0.0724	0.9212	-0.0941	1.059	0.1054	-0.3815	0.5914	0.274	0.2206	0.0188	-0.5931	-0.1714	-0.3476	0.8901	0.1803	0.1132	0.5856	-0.0588	0.7356	-0.1808	68.4551	25.5833
6	1.0976	-0.171	0.0358	1.9209	-0.2298	1.95	-0.0169	0.0604	-0.0323	0.0746	0.1221	0.1971	0.1878	-0.3584	-0.1239	0.3511	0.0039	0.0742	0.4617	0.0959	0.429	-7.4851	38.6355	6.9472
7	0.8132	-0.3302	-0.0324	1.185	-0.1119	1.6	-0.0425	-0.1902	0.1558	0.314	0.1549	0.0663	-0.2345	-0.174	-0.1169	0.4252	0.1325	0.0911	0.4888	0.0615	0.4603	-6.0513	53.0511	23.9578
8	1.9368	0.2098	0.6159	2.4582	1.9515	2.96	-0.0507	0.064	0.1701	0.176	-0.0124	0.6106	-0.2945	-0.6647	0.0938	0.5213	0.2474	0.143	0.7316	0.2171	0.6899	-21.9696	62.8034	14.9443
9	9.4854	-3.7289	1.2849	1.9787	0.285	1.4031	-0.4919	-1.2166	-0.4842	-0.5523	0.3137	0.1762	0.0281	0.2938	0.1848	1.9268	0.1379	0.1991	1.4428	0.0725	1.4576	-46.0614	61.0342	18.6619
10	0.7926	-0.2864	0.8233	0.7389	-0.5931	2.5713	0.2033	0.4731	0.4277	-0.5754	-0.1295	0.1381	-0.5522	-0.2267	-0.0423	1.094	0.2103	0.0355	1.0564	0.4213	0.9747	-13.9331	78.0407	-43.5794
11	1.0726	0.0208	-0.3354	1.2861	0.5674	1.4003	0.1169	0.1496	0.1072	-0.1586	-0.061	0.4012	-0.1256	-0.5445	-0.0479	0.4302	0.0887	-0.0694	0.8087	0.2512	0.7174	-24.9488	54.4547	-18.9133
12	2.7908	-0.6959	-0.6135	5.8471	-0.6105	1.5545	0.1302	0.32	-0.0196	-0.6244	0.0085	0.2872	-0.2634	-0.6626	-0.1112	0.6541	0.1804	-0.0851	0.8645	0.1956	0.5608	-19.9213	59.9347	-30.2489
13	1.1914	-0.5008	0.2071	1.3299	0.0736	0.0639	-0.042	0.3801	0.5054	-0.3584	-0.029	0.5812	-0.653	-0.8853	0.1113	0.6913	0.3422	-0.0379	1.131	0.2409	0.9562	-32.4117	70.7277	-29.0796
14	0.6081	-0.3155	0.1691	1.7777	0.3718	0.9624	0.1755	0.4697	0.198	-0.5214	-0.0241	0.5241	-0.4048	-0.541	-0.1264	0.8698	0.2216	-0.1236	1.0312	0.3313	0.7833	-20.4613	65.1833	-44.0631

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 136 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 137 through 321 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 322 through 560 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 561 through 685 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 20 through 65 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 66 through 287 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 288 through 498 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 499 through 560 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 561 through 630 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 20 through 65 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 66 through 283 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 284 through 339 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 340 through 397 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 398 through 548 )

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