PDB-8w0h: Crystal structure of Acetyl-CoA synthetase 2 from Candida albican...

ID or keywords:

Entry

Database: PDB / ID: 8w0h

Title

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

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: 2.95 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 (trigonal form)
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	8w0h.cif.gz	772.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8w0h.ent.gz	649.4 KB	Display	PDB format
PDBx/mmJSON format	8w0h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8w0h_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8w0h_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8w0h_validation.xml.gz	65.2 KB	Display
Data in CIF	8w0h_validation.cif.gz	87.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w0/8w0h ftp://data.pdbj.org/pub/pdb/validation_reports/w0/8w0h	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
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	113.915, 113.915, 354.437
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

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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 , 5 types, 16 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#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-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄

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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: 2.92 Å³/Da / Density % sol: 57.81 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Berkeley G9: 0.1 M BIS-TRIS pH 6.5 , 45% PEG 400. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1195 added to the protein prior to crystallization. plate 13752 well G9 drop 1. Puck: PSL-1808, Cryo: Direct.

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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: Nov 23, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 2.95→49.33 Å / Num. obs: 57351 / % possible obs: 100 % / Redundancy: 10.1 % / CC_1/2: 0.997 / R_merge(I) obs: 0.171 / R_pim(I) all: 0.056 / R_rim(I) all: 0.181 / Χ²: 1 / Net I/σ(I): 11.7 / Num. measured all: 579870
Reflection shell	Resolution: 2.95→3.03 Å / % possible obs: 100 % / Redundancy: 9.6 % / R_merge(I) obs: 1.598 / Num. measured all: 40067 / Num. unique obs: 4177 / CC_1/2: 0.579 / R_pim(I) all: 0.543 / R_rim(I) all: 1.689 / Χ²: 1.03 / Net I/σ(I) obs: 1.6

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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: 2.95→49.33 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2235	2980	5.2 %
R_work	0.1875	-	-
obs	0.1894	57263	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.95→49.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15321	0	194	0	15515

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	15893
X-RAY DIFFRACTION	f_angle_d	0.518	21573
X-RAY DIFFRACTION	f_dihedral_angle_d	10.358	5794
X-RAY DIFFRACTION	f_chiral_restr	0.043	2361
X-RAY DIFFRACTION	f_plane_restr	0.004	2764

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 (%)
2.95-3	0.4013	148	0.3517	2580	X-RAY DIFFRACTION	100
3-3.05	0.3538	145	0.3228	2502	X-RAY DIFFRACTION	100
3.05-3.11	0.3188	128	0.3	2552	X-RAY DIFFRACTION	100
3.11-3.17	0.2739	119	0.2527	2588	X-RAY DIFFRACTION	100
3.17-3.23	0.3073	142	0.2386	2519	X-RAY DIFFRACTION	100
3.23-3.3	0.305	143	0.2379	2528	X-RAY DIFFRACTION	100
3.3-3.38	0.2871	142	0.2438	2563	X-RAY DIFFRACTION	100
3.38-3.46	0.2792	119	0.2471	2591	X-RAY DIFFRACTION	100
3.46-3.55	0.293	125	0.2512	2565	X-RAY DIFFRACTION	100
3.56-3.66	0.2572	164	0.2014	2544	X-RAY DIFFRACTION	100
3.66-3.78	0.2363	133	0.1871	2553	X-RAY DIFFRACTION	100
3.78-3.91	0.2098	142	0.172	2584	X-RAY DIFFRACTION	100
3.91-4.07	0.2027	130	0.1611	2584	X-RAY DIFFRACTION	100
4.07-4.25	0.1915	165	0.1576	2534	X-RAY DIFFRACTION	100
4.25-4.48	0.1933	132	0.1504	2601	X-RAY DIFFRACTION	100
4.48-4.76	0.1684	151	0.1359	2590	X-RAY DIFFRACTION	100
4.76-5.13	0.1915	133	0.1482	2603	X-RAY DIFFRACTION	100
5.13-5.64	0.1973	149	0.1703	2619	X-RAY DIFFRACTION	100
5.64-6.46	0.2044	164	0.1848	2598	X-RAY DIFFRACTION	100
6.46-8.13	0.2067	149	0.1886	2688	X-RAY DIFFRACTION	100
8.13-49.33	0.1881	157	0.1569	2797	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	2.3888	0.2441	-1.6141	4.4012	1.6245	4.5625	-0.1427	-0.2186	-0.0363	0.639	0.2828	0.6757	1.0859	-0.2426	-0.1986	1.0493	-0.1192	0.044	0.7413	0.1271	0.7371	31.6805	-84.5358	56.0242
2	4.5501	0.1705	1.4265	4.437	-0.0399	3.1163	0.4294	-0.1084	-0.9564	0.7076	0.2832	0.0051	2.062	0.1637	-0.7294	1.7616	0.0518	-0.1579	0.6984	0.081	0.8209	38.4027	-94.4437	52.1196
3	1.6982	-1.1082	0.0676	1.5026	0.0105	2.0188	0.0974	0.3884	0.0718	-0.1355	-0.1684	-0.6284	-0.0294	0.5175	0.09	0.6145	-0.0883	0.2062	0.7269	-0.044	0.879	89.7352	-39.2797	7.9088
4	1.2705	0.3402	0.1861	2.8256	-0.2278	1.0492	0.1526	-0.2597	-0.3061	0.2994	-0.1517	-0.3433	0.0162	0.0521	-0.0013	0.4396	-0.0822	-0.0295	0.5378	0.0129	0.4781	69.1895	-49.2448	32.5278
5	1.6064	-0.2233	0.2134	1.3788	0.2948	1.5509	0.1417	-0.2794	-0.4434	0.1671	-0.103	-0.4627	0.1258	0.0985	-0.0428	0.4034	-0.115	-0.0809	0.4619	0.01	0.6079	77.768	-51.4789	30.6443
6	1.6201	-0.1826	0.0357	1.5986	0.5886	1.7705	0.0016	0.0431	-0.1351	-0.0379	-0.035	-0.5839	-0.0695	0.38	0.0405	0.4056	-0.124	0.0749	0.55	-0.0309	0.6558	86.5187	-36.1673	21.811
7	1.7387	0.1133	1.7814	1.5586	-0.2067	3.6498	0.1304	-0.4262	-0.3339	0.535	-0.2754	-0.7705	-0.0737	-0.025	0.1545	0.6426	-0.2262	-0.1816	0.7731	0.0718	0.9195	92.1132	-34.0565	43.1849
8	3.6819	-0.9093	-0.2967	3.4286	1.4532	5.8757	0.176	-0.0534	0.2555	-0.0999	-0.1419	-0.0684	-1.1536	0.3959	-0.1304	1.0752	-0.2595	-0.3326	1.0374	0.1455	1.0339	101.4508	-22.5485	47.7161
9	1.7873	0.2492	0.0715	1.2419	-0.0525	0.9062	-0.115	0.0411	0.3448	-0.1948	0.0954	0.1602	-0.1542	-0.0669	0.0244	0.5755	-0.0536	0.0285	0.4905	-0.0508	0.5109	34.8368	-21.7688	13.3428
10	2.5506	0.2163	0.187	2.2218	-0.1221	1.6474	-0.1394	-0.5721	0.2335	0.3933	0.129	0.0771	-0.2288	-0.3126	-0.013	0.7419	-0.0674	0.0705	0.698	-0.2022	0.4465	46.0735	-21.075	39.0993
11	1.5722	0.569	0.1517	1.3536	-0.7292	0.9623	-0.0444	-0.369	0.3052	0.2464	0.0011	0.0372	-0.0882	-0.0549	0.0735	0.5682	-0.0147	0.1036	0.5338	-0.1457	0.4172	43.7193	-21.6509	31.1784
12	1.9495	-0.1008	0.2961	1.9483	-0.0098	1.6002	-0.1145	-0.1239	0.4945	-0.0579	0.0788	0.3091	-0.3892	-0.2127	0.0256	0.5747	0.0658	0.0561	0.4524	-0.0712	0.5533	28.698	-13.0643	21.431
13	0.4374	0.5261	-0.0891	0.9627	1.4629	6.8619	0.17	-0.4104	0.449	0.335	0.05	0.0521	0.3354	-0.5279	-0.2159	0.8502	0.0873	0.0765	0.9013	-0.1048	0.9609	17.9857	-13.7637	34.6298
14	4.0202	-0.4523	-2.3189	0.6333	0.3812	1.4699	0.5899	-0.5797	0.9473	-0.1992	-0.0372	0.1155	0.0204	0.6483	-0.4537	1.1911	-0.046	0.2313	1.0835	-0.3396	1.1682	21.4174	-6.2146	48.2751
15	2.3353	0.9564	-1.2583	5.4471	-0.2605	2.4074	0.1084	0.1481	0.6109	-0.0189	0.0407	1.1913	0.1157	-0.4611	-0.1539	1.2476	-0.0707	0.1783	1.058	-0.0749	1.7529	4.5179	-7.7907	44.2135
16	1.7886	-0.0817	0.0823	1.4832	0.0309	1.2386	0.2225	-0.0992	-0.2309	-0.0377	-0.0411	0.1316	0.1739	-0.1055	-0.1542	0.4658	-0.1143	-0.0302	0.4462	0.0561	0.3953	35.3206	-64.1266	22.3811
17	1.9829	-0.5061	0.3774	1.6364	-0.3436	1.2595	0.0654	-0.4838	-0.2397	0.3342	0.1425	0.2534	-0.0606	-0.2196	-0.1692	0.5406	-0.1311	0.0544	0.6341	0.1337	0.4415	32.6474	-59.5893	38.6018
18	0.8909	-0.0719	0.1062	1.4333	-0.2133	1.7544	0.1944	0.0133	-0.5236	-0.0915	-0.0298	0.3204	0.4273	-0.2978	-0.1266	0.5756	-0.202	-0.1105	0.4109	0.0585	0.6102	32.8668	-77.6491	25.3671
19	0.4889	-0.8262	-1.2102	1.8673	1.828	8.7786	-0.0113	-0.3192	-0.1966	0.2747	0.1433	0.0437	0.6525	0.6757	-0.0604	0.7411	-0.1398	-0.0644	0.5872	0.0894	0.8279	39.3082	-84.873	39.4627

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 585 through 620 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 621 through 683 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 20 through 65 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 66 through 249 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 250 through 397 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 398 through 531 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 532 through 632 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 633 through 685 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 20 through 136 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 137 through 249 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 250 through 339 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 340 through 531 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 532 through 584 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 585 through 633 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 634 through 685 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 20 through 198 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 199 through 339 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 340 through 531 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 532 through 584 )

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