PDB-8g0s: Crystal Structure of Acetyl-CoA synthetase in complex with a cycl...

ID or keywords:

Entry

Database: PDB / ID: 8g0s

Title

Crystal Structure of Acetyl-CoA synthetase in complex with a cyclopentyl ester AMP inhibitor from Cryptococcus neoformans H99 (tetragonal form)

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: 2.9 Å

Authors

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 cyclopentyl ester AMP inhibitor from Cryptococcus neoformans H99 (tetragonal form)
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	Mar 15, 2023	Group: Other / Structure summary Category: audit_author / pdbx_SG_project / pdbx_database_status Item: _pdbx_database_status.SG_entry
Revision 1.2	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	8g0s.cif.gz	718 KB	Display	PDBx/mmCIF format
PDB format	pdb8g0s.ent.gz	598 KB	Display	PDB format
PDBx/mmJSON format	8g0s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8g0s_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8g0s_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8g0s_validation.xml.gz	59.4 KB	Display
Data in CIF	8g0s_validation.cif.gz	80.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g0/8g0s ftp://data.pdbj.org/pub/pdb/validation_reports/g0/8g0s	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)	174.160, 174.160, 158.927
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#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) / References: UniProt: A0A854QMN0
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-YHF / 5'-O-[(S)-(cyclopentyloxy)(hydroxy)phosphoryl]adenosine Mass: 415.338 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₁₅H₂₂N₅O₇P / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.59 Å³/Da / Density % sol: 52.56 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: Morpheus G5 (75% dilution): 15%(v/v) PEG 500 MME, 7.5%(w/v) PEG 20000, 75 mM HEPES/MOPS, pH 7.5, 15 mM Sodium formate, 15 mM Ammonium acetate, 15 mM Sodium citrate tribasic, 15 mM Potassium ...Details: Morpheus G5 (75% dilution): 15%(v/v) PEG 500 MME, 7.5%(w/v) PEG 20000, 75 mM HEPES/MOPS, pH 7.5, 15 mM Sodium formate, 15 mM Ammonium acetate, 15 mM Sodium citrate tribasic, 15 mM Potassium sodium tartrate and 15 mM Sodium oxamate, CrneC.00629.a.FS11.PD00460 at 10 mg/mL. Plate: Liu-S-057, well E3 , HGN1192 soak for 24 hours (1 mM), Puck: PSL-0712, Cryo Morpheus G5 (100%): 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM HEPES/MOPS, pH 7.5, 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic, 20 mM Potassium sodium tartrate and 20 mM Sodium oxamate

Crystal

Density Matthews: 2.59 Å³/Da / Density % sol: 52.56 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: Morpheus G5 (75% dilution): 15%(v/v) PEG 500 MME, 7.5%(w/v) PEG 20000, 75 mM HEPES/MOPS, pH 7.5, 15 mM Sodium formate, 15 mM Ammonium acetate, 15 mM Sodium citrate tribasic, 15 mM Potassium ...

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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: 2.9→174.16 Å / Num. obs: 54700 / % possible obs: 100 % / Redundancy: 20.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.166 / R_pim(I) all: 0.037 / R_rim(I) all: 0.17 / Χ²: 1.01 / Net I/σ(I): 15.9 / Num. measured all: 1134798
Reflection shell	Resolution: 2.9→2.98 Å / % possible obs: 100 % / Redundancy: 22.1 % / R_merge(I) obs: 2.312 / Num. measured all: 87526 / Num. unique obs: 3963 / CC_1/2: 0.796 / R_pim(I) all: 0.498 / R_rim(I) all: 2.365 / Χ²: 0.98 / Net I/σ(I) obs: 2

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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: 2.9→25.34 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2226	2610	4.79 %
R_work	0.1903	-	-
obs	0.1919	54475	99.91 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.9→25.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14086	0	87	2	14175

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	14593
X-RAY DIFFRACTION	f_angle_d	0.678	19910
X-RAY DIFFRACTION	f_dihedral_angle_d	12.21	5261
X-RAY DIFFRACTION	f_chiral_restr	0.05	2157
X-RAY DIFFRACTION	f_plane_restr	0.006	2557

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 (%)
2.9-2.95	0.3481	140	0.3191	2680	X-RAY DIFFRACTION	100
2.95-3.01	0.3583	140	0.3054	2674	X-RAY DIFFRACTION	100
3.01-3.07	0.379	134	0.281	2700	X-RAY DIFFRACTION	100
3.07-3.14	0.3233	142	0.2542	2670	X-RAY DIFFRACTION	100
3.14-3.21	0.2488	138	0.2431	2690	X-RAY DIFFRACTION	100
3.21-3.29	0.2456	123	0.2304	2721	X-RAY DIFFRACTION	100
3.29-3.38	0.2512	149	0.2354	2676	X-RAY DIFFRACTION	100
3.38-3.48	0.2811	129	0.2185	2722	X-RAY DIFFRACTION	100
3.48-3.59	0.2566	149	0.2029	2680	X-RAY DIFFRACTION	100
3.59-3.72	0.227	136	0.2048	2724	X-RAY DIFFRACTION	100
3.72-3.87	0.2227	146	0.1947	2715	X-RAY DIFFRACTION	100
3.87-4.04	0.2337	110	0.1819	2721	X-RAY DIFFRACTION	100
4.04-4.25	0.2091	148	0.166	2723	X-RAY DIFFRACTION	100
4.25-4.52	0.1951	124	0.1584	2756	X-RAY DIFFRACTION	100
4.52-4.87	0.169	112	0.152	2747	X-RAY DIFFRACTION	100
4.87-5.35	0.189	152	0.1583	2764	X-RAY DIFFRACTION	100
5.35-6.12	0.2073	145	0.1825	2767	X-RAY DIFFRACTION	100
6.12-7.67	0.2157	141	0.1961	2810	X-RAY DIFFRACTION	100
7.67-25.34	0.1991	152	0.174	2925	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	4.2593	2.3932	1.5859	3.4635	1.8185	1.8623	0.0232	0.2408	0.5077	-0.0663	-0.2109	0.7185	-0.0577	-0.5933	0.1808	0.5566	0.186	-0.024	0.9992	-0.0019	0.7249	-30.8151	-46.0849	-13.86
2	1.0273	0.3838	0.3503	1.6162	0.3961	2.4235	0.2639	0.0489	-0.2759	0.2467	-0.1802	-0.0003	0.4969	-0.4533	-0.1059	0.4935	-0.0947	-0.0623	0.6216	-0.0932	0.6008	-18.4174	-60.2778	4.4778
3	3.2167	-0.0021	0.8712	2.4381	0.3328	3.2777	0.113	0.4218	-0.3782	-0.2991	0.0094	-0.0749	0.3364	-0.0807	-0.0889	0.5333	0.0371	0.0431	0.8519	-0.1841	0.6751	-14.614	-57.2476	-20.6915
4	5.1997	0.5091	-0.539	6.767	-0.7823	5.1869	0.5489	0.1195	-0.9192	-0.6955	-0.5665	0.606	0.4317	-0.7489	0.0222	0.7992	-0.0245	-0.1032	1.0923	-0.1459	1.1324	-38.691	-78.5766	-25.8587
5	5.4447	2.1135	0.6235	0.9074	0.2074	6.1448	0.354	0.2714	-1.6756	-0.3895	-0.004	-0.0364	0.9491	-0.1676	-0.3175	1.0541	0.0702	-0.221	1.0868	-0.2174	1.385	-36.1662	-87.7784	-29.4951
6	0.8405	0.6992	0.4061	4.4606	1.3646	5.636	0.4558	0.029	-0.5209	-0.0969	0.0018	-0.3705	0.2994	0.8577	-0.4447	0.7885	0.0484	-0.1913	1.0644	-0.1509	1.0548	-24.4434	-79.6226	-26.5996
7	3.0533	0.0393	-1.0934	3.2233	2.4575	8.3348	0.2076	-0.5441	0.2509	0.3842	-0.5633	0.2656	-0.8447	-0.7067	0.3861	1.0275	-0.0301	0.0741	1.0498	-0.0489	1.0095	-17.6022	-19.6162	36.6947
8	1.8576	0.4614	0.2525	1.4235	0.0898	1.9842	0.3221	-0.2054	-0.2761	0.3971	-0.2334	-0.2815	0.2286	0.0791	-0.0893	0.6606	-0.1208	-0.101	0.6158	0.0204	0.6513	9.2345	-37.2669	30.1161
9	5.8063	-0.2861	0.3148	5.7187	1.1363	4.9413	0.472	-0.4679	-0.3442	0.0559	-0.0131	-0.1064	0.2888	-0.4477	-0.4388	0.5942	-0.2087	-0.0094	0.6089	-0.0053	0.5125	-5.4203	-38.2405	31.7878
10	2.9676	-0.5795	1.3134	1.599	0.1323	4.2415	0.2835	-0.44	0.052	0.7661	-0.4385	0.0695	-0.1793	-0.3144	0.1305	0.7962	-0.2763	-0.01	0.7071	0.0165	0.6141	2.5269	-26.483	41.1198
11	3.3869	0.0963	-0.5577	4.1644	-1.3233	3.3664	0.2355	-0.9573	-0.0066	1.2774	0.0111	-0.1166	-0.4861	0.5386	-0.2175	1.2254	-0.3327	0.0146	1.1084	-0.1128	0.713	3.0664	-20.6571	53.018
12	2.902	-0.0559	0.6016	3.9521	1.2847	2.2798	0.4046	-0.8197	0.5006	1.1406	-0.2724	0.0965	0.1354	-0.6383	-0.1784	1.2362	-0.3754	0.1036	1.2258	-0.1465	0.8506	-10.0124	-26.0337	50.2568
13	2.3438	0.1384	-1.2919	4.7425	-1.6061	7.9768	-0.0028	-0.6058	0.4838	0.2234	0.6632	0.5994	-0.1416	-1.1067	-0.6073	0.7255	-0.2561	0.1534	1.1378	-0.1338	0.7886	-25.1418	-37.9792	45.0052
14	3.7878	-0.6554	-0.59	2.5095	-0.0911	3.6318	0.2212	-0.5554	-0.1699	0.6	-0.1713	0.5961	0.0365	-0.4577	-0.0558	1.0244	-0.3651	0.0096	0.9569	-0.0389	0.7523	-17.1653	-42.8608	40.7021
15	4.7807	1.3114	0.0705	5.914	-0.314	7.3035	-0.0677	0.6413	0.7884	-0.5712	0.3061	-0.2194	-1.1667	0.4334	-0.2649	0.7666	0.0928	0.0606	0.6241	-0.0012	0.8037	14.3197	-8.3319	-8.3001
16	1.4104	0.0676	-0.2766	1.9302	0.5343	1.6874	0.1147	0.1378	-0.1277	-0.036	0.0248	-0.4428	0.128	0.3712	-0.1448	0.3797	0.0645	0.015	0.7042	-0.0688	0.7023	16.4691	-40.4806	-3.5435
17	1.1591	0.8679	-0.9258	1.2903	-0.3541	1.9823	-0.0009	0.2743	0.0554	-0.2888	-0.0994	-0.2108	-0.086	0.1406	0.1101	0.68	0.0117	0.1686	0.8869	-0.0625	0.7957	25.0059	-22.2641	-15.6327
18	1.6712	-0.066	-0.1359	1.7031	0.2304	2.2664	0.2875	0.0016	0.0662	-0.0631	-0.0359	-0.5223	-0.635	0.4764	-0.2302	0.6259	-0.14	0.1146	0.9474	-0.1052	0.9077	31.1735	-17.5899	6.64
19	3.3728	-0.9406	-0.1916	5.0565	0.5493	5.1472	-0.2919	-0.6772	-0.743	0.9544	0.3486	0.0581	0.6546	-0.0781	-0.0692	1.1727	-0.0942	0.1037	1.8889	0.0337	1.0216	54.6246	-30.3858	10.1104

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 74 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 75 through 462 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 463 through 545 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 546 through 579 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 580 through 618 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 619 through 677 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 25 through 74 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 75 through 278 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 279 through 316 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 317 through 365 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 366 through 406 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 407 through 462 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 463 through 493 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 494 through 543 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 15 through 74 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 75 through 317 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 318 through 474 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 475 through 551 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 552 through 677 )

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