PDB-8v4o: Crystal structure of Acetyl-CoA synthetase 2 in complex with AMP ...

ID or keywords:

Entry

Database: PDB / ID: 8v4o

Title

Crystal structure of Acetyl-CoA synthetase 2 in complex with AMP 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 from Candida albicans
Authors: Lovell, S. / Liu, L. / 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	8v4o.cif.gz	703.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8v4o.ent.gz	584.8 KB	Display	PDB format
PDBx/mmJSON format	8v4o.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/v4/8v4o ftp://data.pdbj.org/pub/pdb/validation_reports/v4/8v4o	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) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Acetyl-coenzyme A synthetase 2

B: Acetyl-coenzyme A synthetase 2

C: Acetyl-coenzyme A synthetase 2

hetero molecules

230 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)	139.463, 139.463, 544.987
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

#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
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H₂O
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: 3.36 Å³/Da / Density % sol: 63.38 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Berkeley B12: 25% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 200 mM Ammonium sulfate. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM AMP added to the protein prior to ...Details: Berkeley B12: 25% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 200 mM Ammonium sulfate. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM AMP added to the protein prior to crystallization. Plate: 13581 well B12 drop 1. Puck: PSL-1602, Cryo: 10% PEG 200 + 90% well.

Crystal

Density Matthews: 3.36 Å³/Da / Density % sol: 63.38 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Berkeley B12: 25% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 200 mM Ammonium sulfate. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM AMP added to the protein prior 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→49.68 Å / Num. obs: 87373 / % possible obs: 100 % / Redundancy: 19.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.179 / R_pim(I) all: 0.041 / R_rim(I) all: 0.183 / Χ²: 1.01 / Net I/σ(I): 15.3 / Num. measured all: 1732654
Reflection shell	Resolution: 2.7→2.75 Å / % possible obs: 100 % / Redundancy: 19 % / R_merge(I) obs: 2.229 / Num. measured all: 83770 / Num. unique obs: 4413 / CC_1/2: 0.747 / R_pim(I) all: 0.524 / R_rim(I) all: 2.29 / 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→49.68 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2397	4340	4.98 %
R_work	0.215	-	-
obs	0.2162	87175	99.95 %

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→49.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13960	0	122	177	14259

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	14447
X-RAY DIFFRACTION	f_angle_d	0.549	19714
X-RAY DIFFRACTION	f_dihedral_angle_d	12.501	5072
X-RAY DIFFRACTION	f_chiral_restr	0.043	2163
X-RAY DIFFRACTION	f_plane_restr	0.005	2533

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	0.3888	146	0.3872	2721	X-RAY DIFFRACTION	100
2.73-2.76	0.3536	156	0.3409	2662	X-RAY DIFFRACTION	100
2.76-2.8	0.3614	149	0.3276	2731	X-RAY DIFFRACTION	100
2.8-2.83	0.3126	135	0.3133	2685	X-RAY DIFFRACTION	100
2.83-2.87	0.2846	137	0.2986	2710	X-RAY DIFFRACTION	100
2.87-2.91	0.3088	148	0.2934	2740	X-RAY DIFFRACTION	100
2.91-2.95	0.3572	143	0.2914	2702	X-RAY DIFFRACTION	100
2.95-2.99	0.3185	146	0.2889	2673	X-RAY DIFFRACTION	100
2.99-3.04	0.2953	158	0.2839	2726	X-RAY DIFFRACTION	100
3.04-3.09	0.3161	129	0.2785	2725	X-RAY DIFFRACTION	100
3.09-3.14	0.328	148	0.2967	2699	X-RAY DIFFRACTION	100
3.14-3.2	0.3546	143	0.3015	2711	X-RAY DIFFRACTION	100
3.2-3.26	0.2708	161	0.2907	2729	X-RAY DIFFRACTION	100
3.26-3.33	0.2768	131	0.2685	2746	X-RAY DIFFRACTION	100
3.33-3.4	0.3153	129	0.2476	2758	X-RAY DIFFRACTION	100
3.4-3.48	0.2664	159	0.2487	2699	X-RAY DIFFRACTION	100
3.48-3.57	0.278	143	0.229	2747	X-RAY DIFFRACTION	100
3.57-3.66	0.2467	160	0.2208	2718	X-RAY DIFFRACTION	100
3.66-3.77	0.2397	151	0.2172	2753	X-RAY DIFFRACTION	100
3.77-3.89	0.2178	131	0.2169	2758	X-RAY DIFFRACTION	100
3.89-4.03	0.2276	138	0.2031	2742	X-RAY DIFFRACTION	100
4.03-4.19	0.1875	151	0.1788	2771	X-RAY DIFFRACTION	100
4.19-4.38	0.1761	127	0.1652	2800	X-RAY DIFFRACTION	100
4.39-4.62	0.1655	124	0.1576	2792	X-RAY DIFFRACTION	100
4.62-4.9	0.1869	150	0.1556	2783	X-RAY DIFFRACTION	100
4.91-5.28	0.1955	145	0.1696	2817	X-RAY DIFFRACTION	100
5.28-5.81	0.2337	147	0.1917	2847	X-RAY DIFFRACTION	100
5.81-6.65	0.2288	138	0.1932	2866	X-RAY DIFFRACTION	100
6.65-8.38	0.2251	155	0.1929	2900	X-RAY DIFFRACTION	100
8.38-49.68	0.2032	162	0.1878	3124	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	1.0302	-0.0862	-0.6477	0.9561	0.2128	1.9226	-0.0714	0.0254	-0.0319	-0.0539	0.3155	-0.1492	-0.2125	0.3402	-0.2284	0.5314	-0.0825	0.047	0.5722	-0.0077	0.6563	36.2678	32.5087	-21.6033
2	1.0694	0.0579	0.1021	0.878	0.2304	1.3022	0.0117	0.2098	0.087	-0.1595	0.0316	0.0326	0.0263	-0.2137	-0.0189	0.4801	-0.0173	0.0168	0.5083	0.1073	0.4785	5.9061	35.9733	-24.1812
3	1.2105	0.7197	0.2598	1.1448	-0.6763	2.6056	0.1038	0.031	-0.1635	0.0115	-0.1343	0.0831	0.5653	-0.5053	-0.0105	0.6778	-0.1327	-0.0167	0.7861	0.0528	0.6279	-5.2947	17.4275	-26.7101
4	1.3925	0.1168	-0.2686	0.9312	0.2315	1.2465	0.0177	0.2938	-0.0071	-0.2128	0.0858	0.0745	0.0738	-0.3084	-0.1065	0.535	-0.0514	0.0029	0.5543	0.0816	0.466	8.351	28.2093	-29.5673
5	1.2897	0.1781	0.576	0.8219	0.1165	1.3202	-0.0422	0.3386	-0.2485	-0.3147	0.2571	-0.228	0.462	0.146	-0.1683	0.7196	-0.0551	0.1227	0.6015	0.0173	0.5663	28.7369	19.2894	-36.1736
6	0.6377	-0.3851	-0.0768	1.0278	0.0055	1.4443	-0.1323	-0.0474	-0.1167	0.0509	0.1525	-0.0663	0.1012	0.0696	-0.0346	0.4893	-0.0038	0.0246	0.4488	0.0276	0.4641	23.1404	25.14	-10.3605
7	0.7326	0.2627	0.0803	0.9474	-0.0926	0.6101	-0.0069	-0.0891	-0.2302	0.0582	0.1109	-0.01	0.196	-0.0589	-0.0614	0.6895	-0.0016	0.013	0.5979	0.0426	0.6118	18.7299	9.3615	-15.3124
8	1.0399	-0.9155	-0.1147	1.9237	-0.6498	1.1391	-0.002	0.1497	-0.1466	-0.2682	0.1703	0.2338	0.3905	-0.1953	-0.1159	0.8738	-0.0972	-0.0867	0.6082	0.0418	0.6293	10.7374	-3.5794	-18.1012
9	1.0297	0.0027	0.1445	1.4601	-0.7762	2.407	-0.1818	0.2484	0.0686	-0.1656	-0.2745	-0.4421	-0.6416	0.644	0.36	0.8172	-0.0761	0.0016	0.6598	0.0536	0.6787	22.3522	-8.1201	-10.7831
10	0.6676	-0.1831	-0.2882	1.0928	0.2596	1.2994	-0.0362	-0.0363	0.0963	0.0762	0.0756	0.0557	0.0059	-0.1902	-0.035	0.4002	0.0555	0.0753	0.512	0.1243	0.5059	-6.34	49.4082	15.9278
11	0.9204	-0.321	-0.0958	0.1276	0.13	0.4551	-0.2514	-0.0588	-0.0029	0.0321	0.0446	0.3214	0.3492	-0.3417	0.1295	0.8687	0.154	0.1634	0.8587	0.0949	0.9091	-32.2996	63.1999	22.0512
12	0.8719	-0.8236	0.6408	1.7851	-1.1665	2.2602	-0.8204	-0.033	-1.0122	-0.1363	0.521	-0.0714	0.3168	-0.4896	0.2072	1.0973	-0.051	0.3338	0.791	0.0042	1.3892	-45.9455	53.6263	17.3717
13	0.3845	-0.1797	0.0226	0.1695	-0.2344	0.8207	0.2241	0.5271	0.6731	-0.6483	-0.0224	0.0491	-0.7166	-0.6036	-0.2493	1.2252	0.2757	0.1002	1.1056	0.4003	1.0528	-12.909	78.0197	-43.0776
14	0.8999	-0.1787	-0.1916	0.9698	0.151	0.4996	0.2492	0.3923	0.2515	-0.3526	-0.0461	-0.0077	-0.4175	-0.2017	-0.1597	0.7452	0.1684	0.0649	0.8885	0.2863	0.7691	-11.2274	61.9819	-23.4508
15	1.276	0.0273	-0.3011	0.7826	0.0751	0.9786	0.0831	0.242	0.1112	-0.1638	-0.0963	0.2705	-0.2231	-0.5323	-0.0182	0.5554	0.169	-0.0705	1.0105	0.1332	0.8331	-29.8677	51.3676	-18.4412
16	1.0822	-0.354	-0.3537	0.717	0.4039	0.7378	0.1929	0.2968	0.2641	-0.1544	-0.1527	0.1597	-0.1541	-0.5801	-0.0537	0.6084	0.1825	-0.067	0.9881	0.1952	0.8155	-25.4558	59.8251	-22.0187
17	0.1853	-0.0147	-0.2603	0.8237	0.1199	0.8644	0.0093	0.4722	0.6377	-0.3143	0.0922	0.3662	-0.4312	-0.836	-0.0638	1.1404	0.5681	0.0492	1.3468	0.488	1.3337	-34.6071	77.3251	-31.6547
18	0.9914	0.0361	0.3426	0.682	-0.1718	0.3023	0.0686	0.4082	0.4937	-0.6042	0.012	0.5259	-0.7279	-0.4434	-0.078	1.2304	0.3904	-0.0523	1.3583	0.4559	1.0425	-20.0319	69.1835	-45.2109
19	0.3946	0.0708	-0.042	1.2872	-0.0226	0.9471	0.0786	0.6067	0.3014	-0.4616	0.3406	0.4909	-0.3619	-0.4585	-0.4296	0.9701	0.2151	-0.1318	1.1922	0.2881	0.8402	-15.0431	54.6486	-45.0181

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 387 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 388 through 437 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 438 through 531 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 532 through 584 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 585 through 645 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 646 through 684 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 21 through 532 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 533 through 587 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 588 through 681 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 21 through 65 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 66 through 136 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 137 through 249 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 250 through 370 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 371 through 411 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 412 through 498 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 499 through 548 )

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