PDB-8w0l: Crystal structure of Acetyl-CoA synthetase 2 from Candida albican...

ID or keywords:

Entry

Database: PDB / ID: 8w0l

Title

Crystal structure of Acetyl-CoA synthetase 2 from Candida albicans in complex with a propyne AMP ester inhibitor and CoA

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: 2.75 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 and CoA
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	8w0l.cif.gz	731 KB	Display	PDBx/mmCIF format
PDB format	pdb8w0l.ent.gz	611.5 KB	Display	PDB format
PDBx/mmJSON format	8w0l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8w0l_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	8w0l_full_validation.pdf.gz	2.1 MB	Display
Data in XML	8w0l_validation.xml.gz	62.7 KB	Display
Data in CIF	8w0l_validation.cif.gz	85.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w0/8w0l ftp://data.pdbj.org/pub/pdb/validation_reports/w0/8w0l	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) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Acetyl-coenzyme A synthetase 2

B: Acetyl-coenzyme A synthetase 2

C: Acetyl-coenzyme A synthetase 2

hetero molecules

233 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)	139.179, 139.179, 543.690
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 , 7 types, 95 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-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO₄
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 66 / 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 B12: 200 mM Ammonium sulfate, 25% (w/v) PEG 3350, 100 mM HEPES pH 7.5. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1196 and 2mM CoA added to the protein prior to crystallization. ...Details: Berkeley B12: 200 mM Ammonium sulfate, 25% (w/v) PEG 3350, 100 mM HEPES pH 7.5. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1196 and 2mM CoA added to the protein prior to crystallization. plate 13753 well B12 drop 2. Puck: PSL-1314, 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 B12: 200 mM Ammonium sulfate, 25% (w/v) PEG 3350, 100 mM HEPES pH 7.5. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1196 and 2mM CoA added to the protein prior to crystallization. ...

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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: 2.75→48.62 Å / Num. obs: 82254 / % possible obs: 100 % / Redundancy: 20 % / CC_1/2: 0.999 / R_merge(I) obs: 0.18 / R_pim(I) all: 0.041 / R_rim(I) all: 0.185 / Χ²: 1.01 / Net I/σ(I): 15.2 / Num. measured all: 1641529
Reflection shell	Resolution: 2.75→2.82 Å / % possible obs: 100 % / Redundancy: 21.1 % / R_merge(I) obs: 2.487 / Num. measured all: 125188 / Num. unique obs: 5931 / CC_1/2: 0.823 / R_pim(I) all: 0.55 / R_rim(I) all: 2.547 / 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: 2.75→48.62 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2394	4105	5.01 %
R_work	0.2025	-	-
obs	0.2043	82003	99.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.75→48.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14375	0	283	66	14724

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	15020
X-RAY DIFFRACTION	f_angle_d	0.813	20458
X-RAY DIFFRACTION	f_dihedral_angle_d	11.326	5450
X-RAY DIFFRACTION	f_chiral_restr	0.05	2221
X-RAY DIFFRACTION	f_plane_restr	0.007	2604

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 (%)
2.75-2.78	0.3865	147	0.3399	2642	X-RAY DIFFRACTION	100
2.78-2.82	0.2936	144	0.2957	2583	X-RAY DIFFRACTION	100
2.82-2.85	0.3813	146	0.2902	2630	X-RAY DIFFRACTION	100
2.85-2.89	0.3032	125	0.2841	2654	X-RAY DIFFRACTION	100
2.89-2.93	0.2974	128	0.2758	2638	X-RAY DIFFRACTION	100
2.93-2.97	0.2971	156	0.2737	2646	X-RAY DIFFRACTION	100
2.97-3.02	0.3119	144	0.2696	2629	X-RAY DIFFRACTION	100
3.02-3.06	0.2767	139	0.2643	2601	X-RAY DIFFRACTION	100
3.06-3.11	0.3168	142	0.2725	2646	X-RAY DIFFRACTION	100
3.11-3.17	0.283	130	0.2721	2669	X-RAY DIFFRACTION	100
3.17-3.22	0.3478	152	0.2658	2621	X-RAY DIFFRACTION	100
3.22-3.29	0.3314	144	0.2578	2633	X-RAY DIFFRACTION	100
3.29-3.35	0.331	139	0.2398	2652	X-RAY DIFFRACTION	100
3.35-3.43	0.2732	138	0.226	2649	X-RAY DIFFRACTION	100
3.43-3.51	0.2821	132	0.2228	2684	X-RAY DIFFRACTION	100
3.51-3.59	0.2723	135	0.2078	2645	X-RAY DIFFRACTION	100
3.59-3.69	0.2431	135	0.2109	2680	X-RAY DIFFRACTION	100
3.69-3.8	0.2412	127	0.2088	2670	X-RAY DIFFRACTION	100
3.8-3.92	0.2174	143	0.1963	2677	X-RAY DIFFRACTION	100
3.92-4.06	0.247	142	0.1773	2670	X-RAY DIFFRACTION	100
4.06-4.22	0.1798	142	0.1676	2722	X-RAY DIFFRACTION	100
4.22-4.42	0.2121	128	0.1643	2676	X-RAY DIFFRACTION	100
4.42-4.65	0.1835	148	0.157	2743	X-RAY DIFFRACTION	100
4.65-4.94	0.1906	143	0.1536	2701	X-RAY DIFFRACTION	100
4.94-5.32	0.1806	134	0.1645	2752	X-RAY DIFFRACTION	100
5.32-5.86	0.2292	149	0.18	2752	X-RAY DIFFRACTION	100
5.86-6.7	0.2363	133	0.1855	2799	X-RAY DIFFRACTION	100
6.7-8.43	0.2403	171	0.1961	2797	X-RAY DIFFRACTION	100
8.44-48.62	0.2035	169	0.1989	3037	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	1.3559	-0.1025	-0.2758	1.7894	-0.0202	3.3507	0.0168	0.2674	0.0896	-0.1678	0.1695	-0.3759	-0.1769	0.8158	-0.1223	0.5733	-0.0854	0.0771	0.8097	-0.0853	0.8058	36.0426	32.5138	-22.2666
2	1.567	0.1884	0.212	1.0413	0.153	2.5901	0.0021	0.2448	0.1423	-0.1552	0.109	0.0932	-0.0395	-0.223	-0.1215	0.6215	-0.0421	0.0109	0.5858	0.1109	0.6138	5.6461	35.673	-24.5151
3	2.6122	0.4963	0.0869	1.4549	-1.0841	3.4499	-0.0543	0.1086	-0.2616	-0.1208	0.0646	0.1154	0.754	-0.7194	-0.0292	0.7952	-0.2236	-0.0261	0.8064	0.0435	0.6808	-5.4685	17.0908	-26.8907
4	0.9697	-0.0545	-0.0677	1.0065	-0.0855	2.0882	-0.0349	0.149	-0.0293	-0.2271	0.1038	-0.0345	0.2768	-0.0346	-0.0746	0.5556	-0.0781	0.0305	0.4209	0.002	0.5211	17.562	24.5087	-23.67
5	8.9772	-1.4492	-2.7361	7.3064	-4.7264	5.2477	-0.1526	0.177	-0.8597	-0.4428	0.3778	0.3721	0.3708	-0.4198	-0.3441	0.9291	-0.0665	-0.0963	0.5543	-0.0711	0.6332	10.0094	-3.3236	-17.8248
6	4.0682	-4.3354	1.756	8.7354	-5.7257	4.7476	0.0447	0.2184	-0.1771	-0.3577	-0.1256	-0.0246	0.3756	0.1072	0.1211	0.7702	-0.1209	0.0218	0.4427	-0.0447	0.532	15.6827	-5.9805	-14.3825
7	0.9539	-0.32	-0.1902	1.3297	0.1765	1.6539	-0.0346	-0.0644	0.1065	0.1444	0.1631	0.0294	-0.1602	-0.3171	-0.1191	0.4904	0.0989	0.1003	0.527	0.1083	0.5884	-6.6964	49.1085	15.7226
8	3.3486	-0.3257	0.2887	0.4822	0.4742	0.555	-0.483	-0.5174	-0.4417	-0.2874	-0.027	0.297	0.4097	-0.5732	0.46	1.3008	0.0926	0.2264	1.0306	0.1019	1.0591	-37.9001	61.3727	20.1614
9	0.958	-0.1147	0.1767	0.4499	-0.2378	1.1301	0.0467	0.5683	0.4463	-0.5891	-0.1382	0.2654	-0.7203	-0.2414	-0.0147	1.4971	0.2732	0.0279	1.2022	0.4486	1.1066	-13.5247	77.8069	-43.9504
10	1.064	0.085	-0.3831	1.2382	0.6306	1.9743	0.1154	0.1083	0.1672	-0.2632	-0.1081	0.2643	-0.4298	-0.3295	-0.017	0.7423	0.1565	-0.0215	0.9471	0.2217	0.9029	-18.0799	58.5651	-20.5341
11	1.3163	0.3484	-0.1465	1.3102	1.159	2.177	0.05	0.1084	-0.1073	-0.1381	-0.2632	0.4864	0.0094	-0.9735	0.2143	0.5923	0.1092	-0.1079	1.1723	0.1359	0.9862	-34.5746	48.3731	-16.5355
12	2.2506	-0.9067	-0.0022	2.3548	-0.0737	1.2328	0.136	0.2837	-0.0148	-0.4627	-0.0859	0.4418	-0.3797	-0.7265	-0.0455	0.8026	0.2618	-0.0741	1.0125	0.2294	0.7933	-22.9776	62.4673	-28.9839
13	1.036	-0.4146	0.0113	1.2443	0.3563	0.9367	0.16	0.5067	0.2756	-0.3246	-0.052	0.3807	-0.5574	-0.7013	-0.1148	1.1157	0.3262	-0.0966	1.1305	0.3475	0.9108	-22.7699	66.589	-41.199
14	2.5136	0.9146	-0.0338	1.1512	0.7548	0.7042	0.1109	0.5812	0.1159	-0.034	-0.0953	0.0391	-0.315	-0.497	0.062	1.2852	0.2021	-0.1807	1.3331	0.2897	1.0532	-27.1821	56.9134	-48.2654
15	2.9872	-0.0408	-1.8905	1.1281	-1.6096	3.5793	-1.0165	0.1607	0.0083	-0.0639	0.283	-0.3703	-0.5753	-0.6548	0.5581	1.5633	-0.0656	-0.3903	1.5956	0.0957	1.4693	-42.3547	49.4093	-44.1847

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 20 through 65 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 66 through 198 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 199 through 249 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 250 through 560 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 561 through 606 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 607 through 685 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 20 through 531 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 532 through 655 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 20 through 65 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 66 through 198 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 199 through 283 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 284 through 370 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 371 through 531 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 532 through 570 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 571 through 624 )

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