PDB-8v4r: Crystal structure of Acetyl-CoA synthetase 2 in complex with AMP ...

ID or keywords:

Entry

Database: PDB / ID: 8v4r

Title

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

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 /

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 in complex with AMP and CoA from Candida albicans
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Nov 29, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 6, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8v4r.cif.gz	728.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8v4r.ent.gz	606.2 KB	Display	PDB format
PDBx/mmJSON format	8v4r.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/v4/8v4r ftp://data.pdbj.org/pub/pdb/validation_reports/v4/8v4r	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) #154 - Oct 2012 Citric Acid Cycle similarity (2) #4 - Apr 2000 Collagen similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#78 - Jun 2006
Luciferase
similarity (6)
#154 - Oct 2012
Citric Acid Cycle
similarity (2)
#4 - Apr 2000
Collagen
similarity (1)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#24 - Dec 2001
Glycogen Phosphorylase
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#93 - Sep 2007
Citrate Synthase
similarity (1)
#116 - Aug 2009
Sulfotransferases
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
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

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)	139.407, 139.407, 542.252
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 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, 50 molecules

#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical	ChemComp-COA / COENZYME A / Coenzyme A Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-ACY / ACETIC ACID / Acetic acid Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 41 / 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: 63.17 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Berkeley D2: 29% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 200 mM Potassium sodium tartrate. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM ADP, acetate and CoA added to ...Details: Berkeley D2: 29% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 200 mM Potassium sodium tartrate. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM ADP, acetate and CoA added to the protein prior to crystallization. Plate: 13581 well D2 drop 3. Puck: PSL-1608, Cryo: 20% PEG 200 + 80% Berkeley D2.

Crystal

Density Matthews: 3.34 Å³/Da / Density % sol: 63.17 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Berkeley D2: 29% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 200 mM Potassium sodium tartrate. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM ADP, acetate and CoA added to ...

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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: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 8, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.7→49.46 Å / Num. obs: 86857 / % possible obs: 100 % / Redundancy: 20 % / CC_1/2: 0.999 / R_merge(I) obs: 0.185 / R_pim(I) all: 0.042 / R_rim(I) all: 0.189 / Χ²: 1 / Net I/σ(I): 14.5 / Num. measured all: 1734018
Reflection shell	Resolution: 2.7→2.75 Å / % possible obs: 100 % / Redundancy: 19.1 % / R_merge(I) obs: 2.352 / Num. measured all: 86390 / Num. unique obs: 4524 / CC_1/2: 0.8 / R_pim(I) all: 0.551 / R_rim(I) all: 2.416 / Χ²: 0.99 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	1.21rc1_5162	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→49.46 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2309	4353	5.03 %
R_work	0.2063	-	-
obs	0.2075	86612	99.89 %

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→49.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14387	0	195	41	14623

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	14968
X-RAY DIFFRACTION	f_angle_d	0.617	20401
X-RAY DIFFRACTION	f_dihedral_angle_d	11.931	5386
X-RAY DIFFRACTION	f_chiral_restr	0.045	2237
X-RAY DIFFRACTION	f_plane_restr	0.004	2605

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	0.3435	154	0.345	2688	X-RAY DIFFRACTION	100
2.73-2.76	0.3706	136	0.3313	2659	X-RAY DIFFRACTION	100
2.76-2.8	0.3206	142	0.3091	2705	X-RAY DIFFRACTION	100
2.8-2.83	0.2776	137	0.2949	2689	X-RAY DIFFRACTION	100
2.83-2.87	0.3204	147	0.293	2670	X-RAY DIFFRACTION	100
2.87-2.91	0.3181	123	0.2857	2742	X-RAY DIFFRACTION	100
2.91-2.95	0.3711	157	0.2837	2655	X-RAY DIFFRACTION	100
2.95-2.99	0.3113	137	0.2792	2689	X-RAY DIFFRACTION	100
2.99-3.04	0.2947	157	0.2766	2688	X-RAY DIFFRACTION	100
3.04-3.09	0.3154	134	0.276	2710	X-RAY DIFFRACTION	100
3.09-3.14	0.3231	167	0.2954	2653	X-RAY DIFFRACTION	100
3.14-3.2	0.3261	157	0.2865	2701	X-RAY DIFFRACTION	100
3.2-3.26	0.3537	121	0.2662	2728	X-RAY DIFFRACTION	100
3.26-3.33	0.2282	148	0.2505	2698	X-RAY DIFFRACTION	100
3.33-3.4	0.2744	120	0.232	2745	X-RAY DIFFRACTION	100
3.4-3.48	0.276	140	0.2334	2719	X-RAY DIFFRACTION	100
3.48-3.57	0.2252	133	0.2081	2730	X-RAY DIFFRACTION	100
3.57-3.66	0.2763	143	0.21	2737	X-RAY DIFFRACTION	100
3.66-3.77	0.2112	158	0.2135	2717	X-RAY DIFFRACTION	100
3.77-3.89	0.2193	173	0.1984	2688	X-RAY DIFFRACTION	100
3.89-4.03	0.2167	146	0.1854	2726	X-RAY DIFFRACTION	100
4.03-4.19	0.189	157	0.1655	2744	X-RAY DIFFRACTION	100
4.19-4.38	0.1477	150	0.1582	2748	X-RAY DIFFRACTION	100
4.38-4.62	0.1946	145	0.1454	2766	X-RAY DIFFRACTION	100
4.62-4.9	0.1832	142	0.1516	2779	X-RAY DIFFRACTION	100
4.9-5.28	0.1566	149	0.1605	2796	X-RAY DIFFRACTION	100
5.28-5.81	0.2051	124	0.1811	2853	X-RAY DIFFRACTION	100
5.81-6.65	0.1991	135	0.1906	2847	X-RAY DIFFRACTION	100
6.65-8.38	0.2171	152	0.2089	2891	X-RAY DIFFRACTION	100
8.38-49.46	0.2359	169	0.1926	3098	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	1.0429	-0.0514	0.1619	0.8867	0.2045	1.9573	-0.0248	0.1393	0.0887	0.0057	0.132	-0.1602	-0.0621	0.3026	-0.0774	0.6428	-0.0883	0.0663	0.4894	0.03	0.6499	22.2658	36.7573	-21.5109
2	1.4813	0.0805	-0.0499	1.0524	0.2272	2.3224	0.0093	0.1746	-0.1477	-0.071	0.0175	0.1602	0.2783	-0.3538	-0.0783	0.608	-0.0974	0.0104	0.5484	0.0588	0.636	-2.2316	24.2441	-27.385
3	1.2306	0.1307	-0.2997	1.0827	0.0092	1.6034	-0.0653	0.1825	-0.056	-0.1859	0.0871	0.0097	0.1604	-0.0015	-0.0579	0.6006	-0.0747	0.03	0.4385	0.0256	0.5446	13.7885	25.3433	-31.0253
4	1.3223	-0.2245	-0.2006	0.8996	-0.1138	1.9773	-0.0751	-0.0609	-0.127	0.1364	0.1218	-0.0505	0.0951	0.2643	-0.0424	0.5936	-0.024	0.0497	0.4413	-0.0215	0.6039	24.951	23.072	-12.4828
5	5.3816	-0.8828	-1.5956	2.6309	-0.3132	4.489	0.0463	-0.0539	-0.3602	-0.0103	0.0451	0.3707	0.1739	-0.3205	-0.0814	0.7664	-0.0105	-0.0417	0.5064	0.0622	0.7308	10.8477	-3.2652	-17.9394
6	3.0087	-1.3299	-0.5087	4.8832	-3.3031	3.6196	-0.0533	0.2752	-0.142	-0.3611	0.2056	-0.0867	0.1124	-0.0391	-0.1181	0.7909	-0.0649	-0.0363	0.5701	-0.0004	0.6839	16.2867	-6.2138	-14.7197
7	0.8424	-0.4282	-0.2034	1.0163	0.1195	1.3803	-0.0193	-0.0774	0.1243	0.1218	0.1561	0.0385	-0.1099	-0.2559	-0.1286	0.5407	0.0716	0.1386	0.4382	0.0894	0.6035	-5.9769	49.2326	15.6838
8	0.414	-0.0819	-0.3467	0.6076	-0.6354	1.143	0.0702	0.4151	0.1075	0.3497	0.1334	0.9665	0.4503	-0.7609	-0.1655	1.1328	0.0258	0.1545	0.9972	0.0268	1.1649	-25.2293	47.7181	27.7012
9	1.0742	0.1626	-0.2461	0.9808	0.1353	1.2159	0.1014	0.138	0.1624	-0.2477	-0.0435	0.2336	-0.2843	-0.3305	-0.094	0.6442	0.1635	0.0059	0.7796	0.2208	0.8405	-21.7942	58.5758	-23.6771
10	2.7128	-0.9509	-0.1182	3.2068	-0.6532	1.7613	0.1883	0.3798	0.0126	-0.1638	-0.0275	0.2136	-0.1901	-0.1978	-0.0764	0.6747	0.1056	0.0147	0.7434	0.204	0.7783	-16.681	55.2054	-31.7247
11	1.2581	-0.2035	-0.1474	0.6106	0.6628	0.8868	0.0883	0.3541	0.3034	-0.3009	0.0238	0.3618	-0.45	-0.5827	-0.1203	0.9294	0.2352	-0.018	0.9033	0.3132	0.9435	-23.025	66.6535	-38.1437
12	1.1396	-0.0794	0.3359	1.0283	1.0579	1.2415	0.0334	0.5126	0.2878	-0.1367	-0.0163	0.4596	-0.094	-0.4794	-0.089	1.2273	0.1375	-0.1295	1.1937	0.307	1.1123	-26.522	56.611	-48.2586
13	2.0852	-0.7107	-0.1692	0.257	0.0249	4.5251	-0.6872	0.2489	-0.1651	-0.0969	-0.3966	-0.2667	-0.445	-0.1043	1.1456	1.3204	-0.0351	-0.1628	1.4202	0.1227	1.6704	-42.3552	49.2207	-46.1457

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 431 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 432 through 560 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 561 through 605 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 606 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 633 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 20 through 283 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 284 through 323 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 324 through 531 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 532 through 570 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 571 through 633 )

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