PDB-8v5g: Crystal Structure of Acetyl-CoA synthetase from Cryptococcus neof...

ID or keywords:

Entry

Database: PDB / ID: 8v5g

Title

Crystal Structure of Acetyl-CoA synthetase from Cryptococcus neoformans H99 in complex with an ethylsulfamide AMP inhibitor

Components

Acetyl-coenzyme A synthetase

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 / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Cryptococcus neoformans var. grubii (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 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 from Cryptococcus neoformans H99 in complex with an ethylsulfamide AMP inhibitor
Authors: Lovell, S. / Liu, L. / Battaile, K.P.

History

Deposition	Nov 30, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 13, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8v5g.cif.gz	706.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8v5g.ent.gz	587.4 KB	Display	PDB format
PDBx/mmJSON format	8v5g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8v5g_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	8v5g_full_validation.pdf.gz	1.2 MB	Display
Data in XML	8v5g_validation.xml.gz	60.5 KB	Display
Data in CIF	8v5g_validation.cif.gz	82.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v5/8v5g ftp://data.pdbj.org/pub/pdb/validation_reports/v5/8v5g	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

233 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)	72.010, 183.850, 84.725
Angle α, β, γ (deg.)	90.00, 93.40, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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 var. grubii (fungus) Gene: CNAG_00797 / Plasmid: CrneC.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J9VFT1
#2: Chemical	ChemComp-YDO / 5'-deoxy-5'-(ethylsulfamamido)adenosine Mass: 373.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₇O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.41 Å³/Da / Density % sol: 48.94 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Proplex B10: 0.15 M ammonium sulfate, 0.1 M MES 6.0, 15 % w/v PEG 4000. CrneC.00629.a.FS11.PD00460 at 10 mg/mL. 2mM HGN-1224 (AMP-ethylsulfamide) added to the protein prior to ...Details: Proplex B10: 0.15 M ammonium sulfate, 0.1 M MES 6.0, 15 % w/v PEG 4000. CrneC.00629.a.FS11.PD00460 at 10 mg/mL. 2mM HGN-1224 (AMP-ethylsulfamide) added to the protein prior to crystallization. Plate: 13642 well B10 drop 1. Puck: PSL-1805, Cryo: 22% PEG 200 + 78% Well.

Crystal

Density Matthews: 2.41 Å³/Da / Density % sol: 48.94 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Proplex B10: 0.15 M ammonium sulfate, 0.1 M MES 6.0, 15 % w/v PEG 4000. CrneC.00629.a.FS11.PD00460 at 10 mg/mL. 2mM HGN-1224 (AMP-ethylsulfamide) 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: 2.5→183.85 Å / Num. obs: 75632 / % possible obs: 99.8 % / Redundancy: 4.4 % / CC_1/2: 0.993 / R_merge(I) obs: 0.122 / R_pim(I) all: 0.065 / R_rim(I) all: 0.139 / Χ²: 0.98 / Net I/σ(I): 8.1 / Num. measured all: 336299
Reflection shell	Resolution: 2.5→2.56 Å / % possible obs: 99.9 % / Redundancy: 4.6 % / R_merge(I) obs: 0.704 / Num. measured all: 25929 / Num. unique obs: 5607 / CC_1/2: 0.771 / R_pim(I) all: 0.366 / R_rim(I) all: 0.796 / Χ²: 0.93 / Net I/σ(I) obs: 2.1

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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: 2.5→76.84 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2738	3713	4.92 %
R_work	0.2323	-	-
obs	0.2344	75417	99.52 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→76.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13769	0	51	111	13931

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	14212
X-RAY DIFFRACTION	f_angle_d	0.769	19384
X-RAY DIFFRACTION	f_dihedral_angle_d	11.138	5056
X-RAY DIFFRACTION	f_chiral_restr	0.049	2087
X-RAY DIFFRACTION	f_plane_restr	0.008	2501

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 (%)
2.5-2.53	0.3309	133	0.297	2626	X-RAY DIFFRACTION	100
2.53-2.56	0.3429	135	0.3062	2713	X-RAY DIFFRACTION	100
2.57-2.6	0.344	141	0.3072	2613	X-RAY DIFFRACTION	100
2.6-2.64	0.3519	125	0.2936	2668	X-RAY DIFFRACTION	100
2.64-2.68	0.3173	131	0.2891	2686	X-RAY DIFFRACTION	100
2.68-2.72	0.3239	117	0.2882	2630	X-RAY DIFFRACTION	100
2.72-2.76	0.3363	143	0.2933	2670	X-RAY DIFFRACTION	100
2.76-2.81	0.338	162	0.2946	2642	X-RAY DIFFRACTION	100
2.81-2.86	0.3417	137	0.3015	2660	X-RAY DIFFRACTION	100
2.86-2.92	0.3531	157	0.311	2648	X-RAY DIFFRACTION	100
2.92-2.98	0.3364	138	0.3095	2611	X-RAY DIFFRACTION	100
2.98-3.04	0.3293	152	0.2801	2643	X-RAY DIFFRACTION	100
3.04-3.11	0.3168	161	0.2665	2658	X-RAY DIFFRACTION	100
3.11-3.19	0.3171	122	0.2785	2665	X-RAY DIFFRACTION	100
3.19-3.28	0.2943	133	0.2553	2681	X-RAY DIFFRACTION	100
3.28-3.37	0.3047	131	0.2549	2634	X-RAY DIFFRACTION	99
3.37-3.48	0.3314	156	0.2585	2633	X-RAY DIFFRACTION	100
3.48-3.61	0.2761	160	0.248	2666	X-RAY DIFFRACTION	100
3.61-3.75	0.2639	117	0.2306	2638	X-RAY DIFFRACTION	100
3.75-3.92	0.2193	175	0.2195	2610	X-RAY DIFFRACTION	99
3.92-4.13	0.2331	125	0.2016	2662	X-RAY DIFFRACTION	99
4.13-4.39	0.2353	134	0.1853	2682	X-RAY DIFFRACTION	99
4.39-4.72	0.2017	108	0.177	2694	X-RAY DIFFRACTION	100
4.72-5.2	0.1965	135	0.1676	2659	X-RAY DIFFRACTION	99
5.2-5.95	0.2076	122	0.1872	2670	X-RAY DIFFRACTION	99
5.95-7.5	0.2533	122	0.2168	2680	X-RAY DIFFRACTION	99
7.5-76.84	0.2773	141	0.197	2662	X-RAY DIFFRACTION	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	1.0042	1.2331	1.0877	3.0122	1.6922	1.516	-0.1955	0.0371	0.0036	-0.8326	0.0852	0.2014	-0.27	-0.0589	0.0507	0.5531	-0.1116	0.0263	0.494	0.0112	0.2388	18.8725	-18.1818	18.0591
2	0.846	1.1151	0.2173	5.9473	1.6568	0.6528	-0.0239	0.0299	-0.2064	0.167	0.1347	-0.0405	-0.034	0.0356	-0.0763	0.3762	-0.0333	0.025	0.3952	0.0404	0.3189	22.0367	-40.0388	22.7774
3	0.8448	-0.385	0.6349	5.0863	-0.1712	3.0556	-0.0954	-0.4343	-0.1534	0.1271	0.5441	1.7126	-0.6889	-0.6333	-0.4031	0.6058	0.0846	0.1513	0.6128	0.1793	0.8127	8.2827	-47.9842	19.3612
4	0.9435	1.1114	0.5884	2.6143	1.5889	1.3955	0.707	-0.1795	-0.5634	1.5052	-0.0036	-1.3995	0.8851	-0.1126	0.0373	0.6608	-0.0714	-0.3339	0.5014	0.0056	0.6131	46.0207	-1.5565	57.8651
5	0.6958	-0.5965	0.4858	1.8859	-1.493	1.7822	-0.2422	-0.7652	-0.0358	1.4769	0.3942	-0.4498	-0.4784	-0.2476	-0.1531	1.4987	0.2455	-0.4711	0.9577	-0.1257	0.9316	53.2907	8.1992	84.7259
6	0.0497	0.1689	-0.0703	0.5361	-0.2373	0.1036	-0.0862	0.1297	0.1668	-0.1585	0.0039	0.0001	-0.1992	0.0155	0.176	2.0768	-0.4919	-0.5602	1.0093	0.4143	0.7913	29.8771	34.2795	11.9493
7	1.3006	0.4888	0.6909	1.6195	0.0589	0.9486	-0.5346	0.0193	0.5976	-1.1401	-0.14	0.8302	-0.7119	-0.13	0.1978	0.7133	0.0172	-0.3012	0.433	-0.0659	0.6032	25.8025	21.6227	35.1804
8	0.2734	0.1818	0.2611	0.9116	0.5091	0.4495	-0.5008	-0.2281	0.8512	-1.2993	-0.647	1.5681	-0.7147	-0.5287	-1.1729	0.4334	0.1825	-0.7084	0.6895	-0.4129	1.3621	15.4369	25.6629	41.609
9	0.0367	0.095	0.1386	0.4926	0.2511	0.5204	-0.1593	0.0308	0.1426	-0.304	-0.0267	0.6237	-0.2262	-0.1452	0.1005	1.6709	0.0999	-1.0185	0.5054	-0.0254	1.6912	20.2102	46.6188	32.3198
10	1.1169	-0.5677	0.156	0.7924	-0.7904	1.0095	0.0408	0.1923	0.2658	0.0995	0.0958	-0.1881	-0.4669	-0.059	1.0496	1.8446	0.0059	-1.3198	0.7929	0.28	1.4314	17.7745	42.2121	20.2193
11	0.7067	-0.0073	-0.1329	0.0583	-0.0248	0.19	-0.2783	0.7265	0.3766	-0.3804	0.1303	0.2473	-0.5865	-0.3552	0.3954	1.6524	0.1408	-1.4523	0.9322	0.0597	1.3752	8.6131	25.1518	13.6385

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 493 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 494 through 602 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 603 through 676 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 11 through 526 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 527 through 654 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 39 through 60 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 61 through 181 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 182 through 365 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 366 through 416 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 417 through 463 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 464 through 539 )

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