PDB-8eps: Crystal Structure of Acetyl-CoA synthetase in complex with an all...

ID or keywords:

Entry

Database: PDB / ID: 8eps

Title

Crystal Structure of Acetyl-CoA synthetase in complex with an allyl 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 /

molecular replacement / Resolution: 2.65 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

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

History

Deposition	Oct 6, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 19, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 22, 2023	Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8eps.cif.gz	752.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8eps.ent.gz	617.8 KB	Display	PDB format
PDBx/mmJSON format	8eps.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/ep/8eps ftp://data.pdbj.org/pub/pdb/validation_reports/ep/8eps	HTTPS FTP

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Related structure data

Related structure data	7l4gS S: Starting model for refinement
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

A: Acetyl-coenzyme A synthetase

hetero molecules

defined by author&software
Evidence: gel filtration
77.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Acetyl-coenzyme A synthetase

hetero molecules

defined by author&software
77.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Acetyl-coenzyme A synthetase

hetero molecules

defined by author&software
77.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.138, 86.889, 105.861
Angle α, β, γ (deg.)	66.220, 73.160, 89.320
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-WPO / 5'-O-{(S)-hydroxy[(prop-2-en-1-yl)oxy]phosphoryl}adenosine Mass: 387.285 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₃H₁₈N₅O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.17 Å³/Da / Density % sol: 43.39 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus F3: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Imidazole/MES, pH 6.5, 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM L-Fucose, 20 mM D-Xylose and 20 mM N-Acetyl-D- ...Details: Morpheus F3: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Imidazole/MES, pH 6.5, 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM L-Fucose, 20 mM D-Xylose and 20 mM N-Acetyl-D-Glucosamine, CrneC.00629.a.FS11.PD00460 at 10 mg/mL. SCRI Tray367F3 HGN1194, Puck: PUCK CIDR002 pin5, Cryo: Direct

Crystal

Density Matthews: 2.17 Å³/Da / Density % sol: 43.39 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus F3: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Imidazole/MES, pH 6.5, 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM L-Fucose, 20 mM D-Xylose and 20 mM N-Acetyl-D- ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.2 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Sep 22, 2022

Radiation

Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.65→46.03 Å / Num. obs: 55144 / % possible obs: 97 % / Redundancy: 2.2 % / B_iso Wilson estimate: 38.07 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.068 / Net I/σ(I): 7.2 / Num. measured all: 121803

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	Net I/σ(I) obs	% possible all
2.65-2.73	2.2	0.343	10095	4529	0.872	2.3	96.8
11.24-46.03	2.4	0.027	1773	749	0.996	19.3	98.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.7.9	data scaling
PHASER		phasing
PHENIX	CrneC.00629.a	refinement
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7L4G

7l4g

Resolution: 2.65→46.03 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 25.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2358	2767	5.02 %
R_work	0.1758	52348	-
obs	0.1788	55115	97 %

Solvent computation

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

Displacement parameters

B_iso max: 123.95 Å² / B_iso mean: 47.6307 Å² / B_iso min: 21.95 Å²

Refinement step

Cycle: final / Resolution: 2.65→46.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14995	0	78	204	15277
B_iso mean	-	-	38.13	38.6	-
Num. residues	-	-	-	-	1948

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.65-2.7	0.3231	156	0.2306	2584	2740	97
2.7-2.74	0.2928	119	0.2188	2632	2751	97
2.74-2.8	0.3164	126	0.2098	2622	2748	97
2.8-2.85	0.2692	154	0.2044	2609	2763	97
2.85-2.92	0.2789	176	0.1989	2577	2753	97
2.92-2.98	0.2904	137	0.2024	2634	2771	97
2.98-3.06	0.2892	133	0.2128	2598	2731	97
3.06-3.14	0.2983	160	0.2118	2617	2777	97
3.14-3.23	0.2854	137	0.1974	2598	2735	96
3.23-3.34	0.2358	163	0.1839	2578	2741	96
3.34-3.46	0.2603	142	0.1815	2595	2737	97
3.46-3.6	0.2178	157	0.1818	2560	2717	96
3.6-3.76	0.2627	110	0.1768	2611	2721	96
3.76-3.96	0.2227	96	0.1723	2642	2738	96
3.96-4.21	0.2175	138	0.1582	2633	2771	98
4.21-4.53	0.1901	149	0.1412	2648	2797	98
4.53-4.99	0.1667	111	0.1349	2647	2758	98
4.99-5.71	0.184	165	0.1528	2630	2795	98
5.71-7.18	0.2237	132	0.1796	2649	2781	97
7.19-46.03	0.2191	106	0.169	2684	2790	98

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	0.7978	-0.0736	-0.1364	0.6108	0.1209	0.1673	0.0359	0.0262	0.0406	-0.0183	-0.0482	-0.0581	0.059	0.1339	-0	0.2464	0.0538	-0.0162	0.347	-0.0048	0.2949	17.1661	-8.5318	-0.2825
2	0.2788	0.0073	-0.0793	0.0173	-0.0119	0.1428	-0.0406	0.0642	-0.0052	0.1782	0.0601	-0.0025	0.1273	-0.2044	0	0.3029	0.0217	0.0187	0.3512	-0.0485	0.3765	-6.4369	-19.2367	-4.7661
3	0.7438	-0.2308	0.0237	0.3525	-0.04	0.682	0.0654	0.0841	-0.0227	-0.0609	-0.071	-0.0588	0.0932	0.1094	-0	0.2701	0.0498	-0.0139	0.3904	-0.0266	0.3281	13.6635	-19.4859	-5.5189
4	0.1076	-0.1435	0.0191	0.1373	-0.0545	0.1302	-0.0175	0.0332	-0.0738	0.0779	0.0222	0.0372	0.1216	0.1987	0	0.32	0.0796	-0.0174	0.4473	-0.0443	0.3166	13.8731	-17.5461	19.5179
5	0.0234	0.0114	-0.0314	0.2689	-0.0414	0.0592	-0.1924	-0.2328	0.0587	0.2203	0.242	0.1426	0.4411	0.3448	-0.0012	0.5413	0.1982	0.0337	0.5351	0.0136	0.3866	22.2165	-35.1315	13.513
6	0.0901	0.0665	-0.0099	0.1133	0.029	0.0205	-0.2123	0.0785	-0.1491	-0.1443	0.1039	0.1179	-0.0327	0.4406	-0.0002	0.7233	0.1713	0.018	0.5329	-0.0858	0.5342	21.839	-50.0394	6.9967
7	0.0521	0.0367	-0.0762	0.1815	-0.0135	0.1142	-0.0479	0.0437	-0.0956	0.3027	0.0196	0.382	-0.0023	0.0891	0	0.6205	0.0548	-0.016	0.4367	0.0657	0.8015	10.655	-42.6658	7.4855
8	0.3219	0.1863	-0.2556	0.0697	-0.079	0.3129	0.026	-0.0744	0.134	-0.0344	0.1066	-0.2062	-0.4125	0.1421	0.0556	0.621	-0.0917	0.0737	0.4043	0.0055	0.3872	0.0714	31.3378	-30.1541
9	0.4336	0.0462	-0.4422	0.6895	0.0425	0.9898	0.1089	0.1176	-0.0486	-0.0144	-0.1403	0.1453	-0.2052	-0.1404	-0	0.3627	0.0846	-0.0414	0.3648	-0.0553	0.2955	-21.576	16.7557	-7.62
10	0.6431	0.2459	-0.5901	0.3067	-0.0851	0.7536	0.1601	0.2311	0.0094	-0.0775	-0.1201	0.0563	-0.4186	-0.2726	0.0169	0.4974	0.1195	-0.0119	0.3508	0.0006	0.2465	-16.3062	29.3163	-24.7099
11	0.0502	-0.1575	-0.0621	0.3857	0.126	0.1934	0.138	0.0321	-0.1437	0.0162	-0.0501	-0.1987	0.0147	0.1041	0	0.3967	0.0516	-0.0016	0.4397	0.0009	0.3529	-3.8977	10.0442	-31.8764
12	0.1951	0.1768	-0.1388	0.0931	-0.1181	0.1403	-0.0899	0.0624	0.0721	-0.1944	0.0299	0.1144	-0.235	-0.0867	-0	0.6499	0.1768	-0.0486	0.5769	0.0168	0.4914	-20.8854	21.6718	-48.4886
13	0.0287	-0.0695	-0.0149	0.1581	-0.0103	0.0416	-0.3368	-0.2031	-0.3013	0.2287	0.0058	0.1838	-0.0276	-0.1655	-0	0.6212	0.05	-0.0308	0.6387	-0.0212	0.4868	-28.9806	15.6429	-42.6726
14	0.2198	0.1176	0.0277	0.2647	0.1435	0.6163	0.0214	-0.1048	0.3312	0.1883	0.0631	-0.2669	-0.0046	0.4315	-0.0044	0.4251	-0.0814	0.0114	0.3425	-0.0549	0.4367	-3.4645	33.9402	34.8869
15	0.7412	-0.0961	0.16	1.2525	0.1065	0.8503	-0.0079	-0.0384	-0.0118	0.1328	0.0737	-0.0091	-0.0085	0.0765	0	0.2491	0.0338	-0.0024	0.344	-0.033	0.2562	-12.1453	12.0892	30.4294
16	0.4701	0.1405	0.0896	0.3134	0.2996	0.3145	0.0251	-0.1337	0.1104	-0.027	0.102	-0.0268	-0.365	0.0049	0	0.3998	0.0912	0.0025	0.3481	-0.0069	0.2955	-27.4291	29.759	35.807
17	0.38	0.4896	0.1035	0.7187	0.186	0.1016	0.1649	-0.1574	0.2254	-0.1117	-0.1309	0.2708	0.5968	0.1998	0.005	0.6503	0.1277	-0.014	0.6301	-0.0862	0.3929	-36.6328	25.4656	47.3762

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 153 )	A	11 - 153
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 154 through 245 )	A	154 - 245
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 246 through 463 )	A	246 - 463
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 464 through 526 )	A	464 - 526
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 527 through 579 )	A	527 - 579
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 580 through 617 )	A	580 - 617
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 618 through 677 )	A	618 - 677
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 10 through 74 )	B	10 - 74
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 75 through 278 )	B	75 - 278
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 279 through 462 )	B	279 - 462
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 463 through 526 )	B	463 - 526
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 527 through 617 )	B	527 - 617
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 618 through 676 )	B	618 - 676
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 11 through 74 )	C	11 - 74
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 75 through 493 )	C	75 - 493
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 494 through 602 )	C	494 - 602
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 603 through 677 )	C	603 - 677

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