PDB-8w0m: Crystal structure of Acetyl-CoA synthetase 2 from Candida albican...

ID or keywords:

Entry

Database: PDB / ID: 8w0m

Title

Crystal structure of Acetyl-CoA synthetase 2 from Candida albicans in complex with a Acetyl Sulfamate 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 / AMP binding / ATP binding
Similarity search - Function

Biological species

Candida albicans (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 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 Acetyl Sulfamate 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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PDBx/mmCIF format	8w0m.cif.gz	660.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8w0m.ent.gz	551 KB	Display	PDB format
PDBx/mmJSON format	8w0m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8w0m_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8w0m_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8w0m_validation.xml.gz	54.2 KB	Display
Data in CIF	8w0m_validation.cif.gz	72.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w0/8w0m ftp://data.pdbj.org/pub/pdb/validation_reports/w0/8w0m	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)	101.399, 115.398, 106.265
Angle α, β, γ (deg.)	90.00, 116.40, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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
#2: Chemical	ChemComp-7RM / 5'-O-(acetylsulfamoyl)adenosine Mass: 388.356 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₂H₁₆N₆O₇S / Feature type: SUBJECT OF INVESTIGATION
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: 2.45 Å³/Da / Density % sol: 49.7 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Berkeley B11: 100 mM Tris pH 8.5, 200 mM Ammonium sulfate, 25% (w/v) PEG 3350. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1076 added to the protein prior to crystallization. Plate: ...Details: Berkeley B11: 100 mM Tris pH 8.5, 200 mM Ammonium sulfate, 25% (w/v) PEG 3350. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1076 added to the protein prior to crystallization. Plate: plate 13749 well C11 drop 1. Puck: PSL-1115, Cryo: 20% PEG 200 + 80% crystallant.

Crystal

Density Matthews: 2.45 Å³/Da / Density % sol: 49.7 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Berkeley B11: 100 mM Tris pH 8.5, 200 mM Ammonium sulfate, 25% (w/v) PEG 3350. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1076 added to the protein prior to crystallization. Plate: ...

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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: 3.1→49.41 Å / Num. obs: 39912 / % possible obs: 99.9 % / Redundancy: 7 % / CC_1/2: 0.995 / R_merge(I) obs: 0.165 / R_pim(I) all: 0.067 / R_rim(I) all: 0.179 / Χ²: 1.01 / Net I/σ(I): 9.2 / Num. measured all: 279234
Reflection shell	Resolution: 3.1→3.18 Å / % possible obs: 100 % / Redundancy: 6.6 % / R_merge(I) obs: 1.44 / Num. measured all: 19321 / Num. unique obs: 2931 / CC_1/2: 0.57 / R_pim(I) all: 0.607 / R_rim(I) all: 1.565 / Χ²: 0.98 / Net I/σ(I) obs: 1.4

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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: 3.1→47.59 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2295	2150	5.39 %
R_work	0.1877	-	-
obs	0.19	39884	99.91 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.1→47.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12967	0	78	0	13045

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	13415
X-RAY DIFFRACTION	f_angle_d	0.52	18275
X-RAY DIFFRACTION	f_dihedral_angle_d	9.304	4793
X-RAY DIFFRACTION	f_chiral_restr	0.044	1969
X-RAY DIFFRACTION	f_plane_restr	0.004	2355

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 (%)
3.1-3.17	0.3622	168	0.3186	2458	X-RAY DIFFRACTION	100
3.17-3.25	0.3304	153	0.2778	2500	X-RAY DIFFRACTION	100
3.25-3.34	0.338	124	0.2585	2542	X-RAY DIFFRACTION	100
3.34-3.44	0.3036	106	0.2403	2513	X-RAY DIFFRACTION	100
3.44-3.55	0.2908	144	0.2199	2513	X-RAY DIFFRACTION	100
3.55-3.68	0.2587	127	0.2007	2517	X-RAY DIFFRACTION	100
3.68-3.82	0.2391	148	0.1892	2515	X-RAY DIFFRACTION	100
3.82-4	0.2183	144	0.169	2487	X-RAY DIFFRACTION	100
4-4.21	0.2009	135	0.1556	2534	X-RAY DIFFRACTION	100
4.21-4.47	0.1735	166	0.1504	2486	X-RAY DIFFRACTION	100
4.47-4.82	0.176	153	0.1388	2525	X-RAY DIFFRACTION	100
4.82-5.3	0.1989	154	0.1512	2516	X-RAY DIFFRACTION	100
5.3-6.06	0.1975	123	0.1755	2544	X-RAY DIFFRACTION	100
6.06-7.64	0.2524	152	0.2059	2525	X-RAY DIFFRACTION	100
7.64-47.59	0.2301	153	0.1965	2559	X-RAY DIFFRACTION	99

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	1.2882	0.0805	-0.3708	1.7517	0.6125	2.1348	0.1636	-0.2088	-0.0443	0.0131	-0.0654	-0.15	-0.1891	0.2916	-0.0276	0.5277	0.0113	0.05	0.4775	0.1018	0.6274	58.6235	28.8022	29.0872
2	3.5603	0.7877	0.4151	3.0909	0.6525	2.0569	0.067	-0.1178	0.0965	-0.0202	-0.0508	0.2381	-0.2765	0.0567	-0.0334	0.5834	-0.0202	0.0777	0.5322	0.0337	0.5053	54.9495	32.1731	34.8632
3	2.077	-0.0604	-0.5023	2.1431	0.763	1.9678	0.1745	-0.5734	-0.0789	0.4551	-0.1484	-0.2417	-0.3173	0.3045	-0.0669	0.7705	-0.1348	-0.0044	0.6832	0.0776	0.5061	59.8438	37.2103	44.1481
4	0.9186	-0.1321	-0.1846	1.0351	0.2765	1.1908	0.0831	-0.6177	-0.7716	0.535	0.1932	0.1414	0.3891	0.3199	-0.0337	1.4671	-0.1906	-0.0118	1.1573	0.1362	1.1072	61.8048	19.8163	55.4158
5	0.6234	0.0677	-0.1932	0.5982	-0.0033	1.5203	0.0469	0.0822	0.1282	0.094	-0.3424	0.3899	-0.5567	-0.5834	0.2049	0.8598	0.274	-0.0536	1.336	-0.0403	1.3344	-3.1726	32.6403	13.1912
6	1.2867	0.0507	-0.1799	1.7441	0.4537	2.3138	-0.0505	-0.1295	0.0109	0.022	-0.1662	0.3347	0.2623	-0.4082	0.1454	0.5454	-0.0133	0.1416	0.521	-0.024	0.7382	23.9278	14.5071	25.0507
7	1.606	0.0665	-0.3647	2.0143	0.0925	2.1114	0.0671	-0.2371	-0.0693	0.1333	-0.2535	0.542	0.0848	-0.6812	0.1637	0.494	-0.0066	0.1051	0.6052	-0.0537	0.7238	13.8425	18.249	26.1195
8	0.967	-0.0362	-0.227	0.8884	0.9122	1.3579	-0.0423	-0.0923	0.5438	0.2503	-0.0126	1.0722	-0.105	-0.9914	0.2463	0.6128	0.0963	0.1559	1.2586	-0.1297	1.4693	-3.1255	21.7758	22.7452
9	2.0919	0.1505	-0.3455	1.9308	0.7712	2.8628	-0.1697	0.1237	0.1091	-0.6011	0.1022	0.5011	-0.0694	-1.1838	0.2142	0.7165	-0.0427	-0.1545	0.9501	-0.0652	0.9931	6.0975	17.1536	1.6474
10	0.6444	0.4819	-0.3052	1.3461	0.2198	1.6467	0.353	0.1129	0.4353	-0.8127	0.0667	-0.0782	-0.304	0.4403	-0.0354	1.686	-0.0817	0.3159	0.6204	0.0836	0.9485	56.0354	42.5758	-23.716
11	1.3819	0.3625	-0.2176	1.5405	0.4842	1.4636	-0.1516	0.0781	-0.1436	-0.4758	0.0445	-0.0171	0.0397	-0.0586	0.0519	0.8994	0.0631	0.0806	0.352	0.044	0.6374	42.7995	14.846	-4.9716
12	1.1353	0.4401	0.7316	1.9015	-0.2793	4.2078	-0.4048	-0.088	-0.5028	-0.5094	0.2664	-0.1464	-0.3944	0.2336	0.0469	0.9482	-0.0243	0.1022	0.3851	-0.0135	0.5852	50.8327	24.6371	-9.7296
13	1.4483	0.1883	-0.7206	1.0835	0.513	2.0081	0.0219	0.2991	0.0228	-0.9622	0.1877	-0.207	-0.2616	0.2136	0.0123	1.3358	-0.0383	0.2509	0.4119	0.0365	0.6588	57.2277	27.4932	-20.0252

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 through 283 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 284 through 339 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 340 through 531 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 532 through 628 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 21 through 65 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 66 through 263 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 264 through 397 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 398 through 467 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 468 through 548 )
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 551 )

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