PDB-8g0t: Crystal Structure of Acetyl-CoA synthetase in complex with a cycl...

ID or keywords:

Entry

Database: PDB / ID: 8g0t

Title

Crystal Structure of Acetyl-CoA synthetase in complex with a cyclopropyl ester AMP inhibitor from Cryptococcus neoformans H99

Components

Acetyl-coenzyme A synthetase

Keywords

LIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE

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

Cryptococcus neoformans (Cryptococcus neoformans serotype A)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.45 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	OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of Acetyl-CoA synthetase in complex with a cyclopropyl ester AMP inhibitor from Cryptococcus neoformans H99
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Staker, B.L.

History

Deposition	Feb 1, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8g0t.cif.gz	782.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8g0t.ent.gz	653.6 KB	Display	PDB format
PDBx/mmJSON format	8g0t.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/g0/8g0t ftp://data.pdbj.org/pub/pdb/validation_reports/g0/8g0t	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

B: Acetyl-coenzyme A synthetase

C: Acetyl-coenzyme A synthetase

hetero molecules

234 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)	62.682, 84.785, 105.471
Angle α, β, γ (deg.)	113.29, 106.90, 90.96
Int Tables number	1
Space group name H-M	P1

#1: Protein	Acetyl-coenzyme A synthetase Mass: 77475.750 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A) Plasmid: CrneC.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A854QMN0
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-YHK / 5'-O-[(R)-(cyclopropyloxy)(hydroxy)phosphoryl]adenosine Mass: 387.285 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₃H₁₈N₅O₇P / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.1 Å³/Da / Density % sol: 41.3 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 12.5% 8K, 0.2M NaCl, 0.1M K/Na phosphate, CrneC.00629.a.FS11.PD00460 at 10 mg/mL. Plate: Liu-S-058 well A2, HGN1193 cocrystallization (1 mM), Puck: PSL-0704, Cryo: 25% PEG200 + 75% crystallant

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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: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 10, 2022
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.45→91.66 Å / Num. obs: 67989 / % possible obs: 98 % / Redundancy: 3.6 % / CC_1/2: 0.997 / R_merge(I) obs: 0.089 / R_pim(I) all: 0.054 / R_rim(I) all: 0.105 / Χ²: 0.97 / Net I/σ(I): 8.1 / Num. measured all: 247316
Reflection shell	Resolution: 2.45→2.51 Å / % possible obs: 97.7 % / Redundancy: 3.8 % / R_merge(I) obs: 0.835 / Num. measured all: 19251 / Num. unique obs: 5045 / CC_1/2: 0.789 / R_pim(I) all: 0.495 / R_rim(I) all: 0.972 / Χ²: 1.02 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.45→25.27 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 35.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2679	3312	4.88 %
R_work	0.2183	-	-
obs	0.2206	67846	97.9 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.45→25.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15290	0	90	60	15440

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	15826
X-RAY DIFFRACTION	f_angle_d	0.519	21558
X-RAY DIFFRACTION	f_dihedral_angle_d	11.602	5716
X-RAY DIFFRACTION	f_chiral_restr	0.044	2340
X-RAY DIFFRACTION	f_plane_restr	0.006	2767

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 (%)
2.45-2.48	0.5056	119	0.3638	2698	X-RAY DIFFRACTION	98
2.48-2.52	0.4273	161	0.3426	2680	X-RAY DIFFRACTION	98
2.52-2.56	0.3622	146	0.3353	2664	X-RAY DIFFRACTION	98
2.56-2.6	0.4708	131	0.3331	2673	X-RAY DIFFRACTION	98
2.6-2.65	0.3999	134	0.3207	2732	X-RAY DIFFRACTION	98
2.65-2.7	0.3227	111	0.303	2693	X-RAY DIFFRACTION	98
2.7-2.75	0.3933	167	0.3	2674	X-RAY DIFFRACTION	98
2.75-2.8	0.3529	143	0.2954	2678	X-RAY DIFFRACTION	98
2.8-2.87	0.3738	132	0.2917	2699	X-RAY DIFFRACTION	98
2.87-2.93	0.3562	183	0.3014	2673	X-RAY DIFFRACTION	98
2.93-3	0.3624	142	0.2844	2680	X-RAY DIFFRACTION	98
3-3.09	0.3629	127	0.2687	2685	X-RAY DIFFRACTION	98
3.09-3.18	0.2771	121	0.2621	2719	X-RAY DIFFRACTION	98
3.18-3.28	0.2759	122	0.2371	2725	X-RAY DIFFRACTION	98
3.28-3.4	0.2959	168	0.2354	2690	X-RAY DIFFRACTION	99
3.4-3.53	0.2966	115	0.2261	2735	X-RAY DIFFRACTION	98
3.53-3.69	0.2493	141	0.2044	2634	X-RAY DIFFRACTION	97
3.69-3.89	0.2133	154	0.198	2659	X-RAY DIFFRACTION	97
3.89-4.13	0.2209	116	0.1844	2627	X-RAY DIFFRACTION	96
4.13-4.45	0.2255	118	0.1786	2694	X-RAY DIFFRACTION	96
4.45-4.89	0.2074	122	0.1643	2641	X-RAY DIFFRACTION	97
4.89-5.59	0.2318	162	0.1761	2739	X-RAY DIFFRACTION	99
5.59-7.02	0.2321	157	0.198	2714	X-RAY DIFFRACTION	99
7.02-25.27	0.1812	120	0.1631	2728	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	2.7892	-2.1179	0.2423	3.1909	0.0544	4.5798	0.3291	0.2006	-0.2254	-0.604	-0.3389	0.2586	0.9465	0.2142	0.0419	0.6352	0.0636	0.0077	0.5038	0.0065	0.4542	12.1079	-19.2719	-15.6904
2	1.2867	-0.1801	-1.0602	1.6689	0.1323	1.4381	0.5444	0.6607	-0.3441	-1.3185	-0.5067	0.0447	1.6272	0.6144	0.0476	1.8927	0.4993	-0.1554	0.7579	-0.248	0.6363	15.2502	-28.9511	-30.783
3	1.2703	-0.6325	-0.8268	1.8338	1.2652	3.8101	0.6967	0.8292	-0.0653	-1.1379	-0.5939	0.1886	0.6238	-0.0841	-0.1027	1.2414	0.3954	-0.1487	0.8082	-0.0688	0.5147	7.6866	-10.55	-35.6882
4	3.8257	0.6724	-1.1266	2.8708	1.8539	2.0603	0.5985	1.2522	-0.3455	-0.6676	-0.4352	-0.287	0.8945	0.6934	-0.1242	2.153	0.8359	0.1721	1.5063	-0.0266	0.8185	27.2155	-20.8514	-52.2156
5	0.1199	-0.1088	0.2454	3.103	-0.1934	5.6629	0.2449	0.4934	0.209	-0.7204	-0.4059	-0.5101	0.6789	0.9396	0.2358	1.2002	0.5346	0.2904	1.4982	0.2039	0.8933	31.551	-11.4364	-38.6019
6	1.7369	0.9988	0.696	1.0385	-1.0573	4.7407	0.0401	-0.5204	-0.3949	0.5402	0.4497	0.4346	1.0893	-0.2485	-0.5589	1.4549	0.3209	0.2727	1.1472	0.4761	1.0613	2.4022	-33.3127	33.1009
7	0.6273	-0.3265	0.4934	1.8907	-0.7096	2.3704	-0.2204	-0.0945	-0.0032	0.6513	0.335	0.1898	0.0174	0.1874	-0.1076	0.6365	0.2394	0.1356	0.797	0.1025	0.5373	11.623	-4.7924	22.2386
8	1.2429	-0.801	1.094	2.5443	-0.8596	2.2362	-0.2812	-0.7085	-0.2266	1.0191	0.4624	0.2753	-0.1656	-0.4298	-0.1039	1.0194	0.3755	0.2099	1.0256	0.1594	0.5623	9.8751	-12.3748	34.43
9	1.9081	-0.6989	-0.1616	1.6104	-0.6889	4.3546	-0.1773	-0.5484	-0.4539	0.5696	0.3944	0.112	0.779	0.3607	-0.234	1.2187	0.3989	0.0862	0.8853	0.1262	0.6305	21.1119	-32.1148	29.714
10	1.9176	1.5356	1.8185	3.9113	-0.2361	4.3537	0.8144	-0.0166	-0.1482	0.1002	-0.9009	-0.0999	0.0916	0.0938	0.0325	1.4101	0.3781	0.0402	1.3818	0.1648	0.675	34.7979	-28.4114	52.7444
11	2.3141	-1.5088	0.697	3.2771	-2.4596	4.2285	0.1651	-0.3999	0.3876	0.1647	0.3652	0.1939	-1.6116	-0.7457	-0.5045	1.8362	0.4198	0.235	1.5229	0.0793	0.7428	35.2555	-21.1355	42.2329
12	2.1695	-1.4907	0.2021	2.7391	-0.9988	2.6781	-0.2054	-0.4749	-0.5995	0.051	0.43	0.7736	-0.1297	-0.6833	-0.0315	0.2815	-0.0701	0.0558	0.6487	0.1528	0.8095	-12.6233	10.34	-2.777
13	1.4706	-0.9379	2.291	4.1214	-1.5059	5.0309	-0.2656	-0.4029	-0.0077	-0.1084	0.3357	-0.309	-0.0178	-0.3497	-0.0388	0.3124	-0.177	0.0555	0.6285	0.0577	0.6931	8.3506	23.1008	-8.93
14	1.377	-2.4593	0.3372	3.6112	-0.3499	2.1792	-0.0232	-0.0824	-0.3313	-0.1347	0.198	0.5414	-0.1428	-0.1088	-0.0333	0.2161	-0.1895	0.0152	0.5522	0.0982	0.6966	-5.8143	14.3387	-7.6133
15	1.9939	-1.8366	-0.162	3.5152	0.009	1.0282	-0.5291	-0.6691	-0.5236	0.6234	0.7828	1.0113	-0.5677	-1.0233	-0.1948	0.4335	0.1625	0.1698	0.987	0.2524	0.92	-20.8097	22.1138	3.172
16	1.1678	-0.1577	-1.1651	4.2488	0.0049	2.9306	-0.6825	-1.1643	-0.0375	0.8925	1.0066	0.6283	-0.7821	-0.9507	-0.2694	1.0764	0.76	0.0843	1.5601	0.115	0.961	-23.5747	34.8619	11.8008
17	4.28	-1.4307	-0.5729	3.6243	-1.909	3.9668	-0.6786	-0.7504	0.561	0.3316	0.7203	0.2416	-0.6148	-0.8922	-0.0202	1.4208	0.6422	-0.1449	1.1945	-0.0204	0.998	-22.9822	49.4829	5.2434
18	2.8776	1.2531	-1.697	3.2911	1.7241	5.4208	-0.5706	-0.2305	0.6206	0.6197	0.4388	-0.1182	-0.7572	0.1723	0.1293	1.0346	0.3297	-0.1924	0.8044	0.0267	0.881	-10.8019	42.5775	6.0541
19	1.8769	0.1977	-0.7629	0.429	0.4334	2.2829	0.6343	0.9093	-0.9246	-1.5654	-0.6765	1.0044	0.7188	-0.2761	-0.062	1.8277	0.1322	-0.4123	0.8029	-0.1169	0.9677	0.1956	-31.3498	-30.7572
20	1.8375	-1.344	0.5916	3.6026	-1.0196	3.1276	0.3115	0.0214	-0.3255	-0.4626	-0.0985	0.1383	0.8531	0.271	-0.1856	0.6381	0.0899	-0.0349	0.494	-0.0477	0.4018	13.1658	-19.9939	-8.4652
21	2.7738	-0.8859	-0.1343	2.1785	-0.9503	2.7	0.2912	0.5604	0.3766	-0.3493	-0.4376	-0.6606	0.6631	1.2768	0.1578	0.5975	0.2203	0.108	0.9417	0.0537	0.6805	30.5419	-12.4837	-10.6524

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 269 through 334 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 335 through 493 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 494 through 555 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 556 through 629 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 630 through 677 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 11 through 74 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 75 through 245 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 246 through 441 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 442 through 579 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 580 through 617 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 618 through 677 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 11 through 205 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 206 through 245 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 246 through 365 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 366 through 526 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 527 through 579 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 580 through 617 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 618 through 677 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 11 through 74 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 75 through 169 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 170 through 268 )

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