PDB-8g0v: Crystal Structure of Acetyl-CoA synthetase in complex with a prop...

ID or keywords:

Entry

Database: PDB / ID: 8g0v

Title

Crystal Structure of Acetyl-CoA synthetase in complex with a propyne 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 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 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 propyne 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

-
Download

PDBx/mmCIF format	8g0v.cif.gz	790.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8g0v.ent.gz	652.4 KB	Display	PDB format
PDBx/mmJSON format	8g0v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8g0v_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	8g0v_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8g0v_validation.xml.gz	70.5 KB	Display
Data in CIF	8g0v_validation.cif.gz	100.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g0/8g0v ftp://data.pdbj.org/pub/pdb/validation_reports/g0/8g0v	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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)	71.079, 81.827, 101.320
Angle α, β, γ (deg.)	70.11, 74.37, 88.37
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 (fungus) / Plasmid: CrneC.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-YHT / 5'-O-{(S)-hydroxy[(prop-2-yn-1-yl)oxy]phosphoryl}adenosine Mass: 385.269 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₃H₁₆N₅O₇P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.3 %
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 A7, HGN1196 cocrystallization (1 mM), Puck: PSL-0704, Cryo: 25% PEG200 + 75% crystallant

-
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: 1.9→91.56 Å / Num. obs: 158139 / % possible obs: 97.3 % / Redundancy: 3.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.057 / R_pim(I) all: 0.035 / R_rim(I) all: 0.067 / Χ²: 0.99 / Net I/σ(I): 11.1 / Num. measured all: 571744
Reflection shell	Resolution: 1.9→1.95 Å / % possible obs: 96.2 % / Redundancy: 3.3 % / R_merge(I) obs: 0.688 / Num. measured all: 37927 / Num. unique obs: 11625 / CC_1/2: 0.752 / R_pim(I) all: 0.458 / R_rim(I) all: 0.832 / Χ²: 1.06 / Net I/σ(I) obs: 1.6

-
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: 1.9→24.67 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2006	7840	4.96 %
R_work	0.1731	-	-
obs	0.1745	158000	97.24 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→24.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15395	0	95	635	16125

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	16148
X-RAY DIFFRACTION	f_angle_d	0.827	22042
X-RAY DIFFRACTION	f_dihedral_angle_d	12.127	5864
X-RAY DIFFRACTION	f_chiral_restr	0.057	2397
X-RAY DIFFRACTION	f_plane_restr	0.008	2848

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 (%)
1.9-1.92	0.3426	253	0.2965	4965	X-RAY DIFFRACTION	96
1.92-1.94	0.3085	276	0.2808	4905	X-RAY DIFFRACTION	96
1.94-1.97	0.3079	291	0.2655	4956	X-RAY DIFFRACTION	97
1.97-1.99	0.2904	261	0.2654	4941	X-RAY DIFFRACTION	96
1.99-2.02	0.2912	248	0.2461	4965	X-RAY DIFFRACTION	96
2.02-2.05	0.2507	254	0.2316	5006	X-RAY DIFFRACTION	97
2.05-2.08	0.2574	258	0.2176	5017	X-RAY DIFFRACTION	97
2.08-2.11	0.2642	265	0.2165	4962	X-RAY DIFFRACTION	97
2.11-2.14	0.2878	264	0.214	5014	X-RAY DIFFRACTION	97
2.14-2.17	0.2415	249	0.1967	5008	X-RAY DIFFRACTION	97
2.17-2.21	0.2311	282	0.1919	5005	X-RAY DIFFRACTION	97
2.21-2.25	0.2245	267	0.1919	4950	X-RAY DIFFRACTION	97
2.25-2.3	0.2388	271	0.1879	5017	X-RAY DIFFRACTION	97
2.3-2.34	0.2478	275	0.1896	4985	X-RAY DIFFRACTION	97
2.34-2.39	0.2305	263	0.182	5045	X-RAY DIFFRACTION	98
2.39-2.45	0.2403	297	0.1846	4982	X-RAY DIFFRACTION	98
2.45-2.51	0.2383	289	0.186	5007	X-RAY DIFFRACTION	98
2.51-2.58	0.2484	227	0.1863	5036	X-RAY DIFFRACTION	98
2.58-2.65	0.216	276	0.1813	5059	X-RAY DIFFRACTION	98
2.65-2.74	0.2163	272	0.1837	5052	X-RAY DIFFRACTION	98
2.74-2.84	0.2063	265	0.1801	5050	X-RAY DIFFRACTION	98
2.84-2.95	0.224	235	0.1928	5038	X-RAY DIFFRACTION	98
2.95-3.08	0.2558	258	0.1995	5007	X-RAY DIFFRACTION	98
3.08-3.25	0.2148	255	0.1903	5008	X-RAY DIFFRACTION	97
3.25-3.45	0.207	238	0.1803	4924	X-RAY DIFFRACTION	96
3.45-3.72	0.1804	243	0.1643	4927	X-RAY DIFFRACTION	95
3.72-4.09	0.1492	261	0.1401	4964	X-RAY DIFFRACTION	96
4.09-4.68	0.1263	263	0.1268	5090	X-RAY DIFFRACTION	99
4.68-5.88	0.1594	250	0.1353	5145	X-RAY DIFFRACTION	99
5.88-24.67	0.163	234	0.1478	5130	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	1.6193	-0.1342	-0.1175	1.8305	0.4428	1.3446	-0.0372	0.0094	-0.2236	0.0798	0.0394	-0.3039	0.2012	0.3008	0.0002	0.2338	0.0629	-0.002	0.4576	0.0614	0.4053	34.6664	-15.5636	6.8543
2	0.8925	-0.0747	0.3017	0.7976	0.1142	1.3132	0.0033	0.1338	-0.0509	-0.1266	-0.0738	0.045	0.0711	-0.064	0.0632	0.2243	0.0247	0.0245	0.3285	-0.0002	0.258	2.0886	-11.2028	-5.5813
3	1.2768	-0.067	0.2313	0.6869	-0.0752	1.2438	0.0158	0.243	-0.172	-0.1493	-0.0551	-0.1217	0.1993	0.2522	0.0262	0.2531	0.0559	0.0619	0.3682	-0.0032	0.2996	23.0489	-19.9874	-5.2213
4	2.228	-0.404	-0.3968	1.1438	0.0187	1.6041	-0.0754	-0.374	-0.0244	0.2058	0.0293	-0.0333	0.0509	0.0746	0.0155	0.2589	0.0227	0.0111	0.3257	0.0397	0.2651	13.8893	-17.7043	19.0201
5	1.8175	-0.5332	-0.3665	1.9672	0.4439	2.1152	-0.0826	0.0545	-0.7542	-0.0345	0.0626	0.4238	0.5659	-0.1223	0.0059	0.5601	0.106	0.0539	0.4659	0.0791	0.745	19.3895	-40.5558	7.9621
6	0.7749	-0.3591	0.1883	1.264	-0.4581	1.1448	-0.0871	0.0916	0.2006	-0.2341	-0.0175	-0.1478	-0.2801	0.2803	0.0981	0.4413	-0.0954	-0.0415	0.3976	0.0679	0.3532	0.9816	26.7274	-21.9466
7	1.1401	0.2501	0.236	1.1249	0.1719	1.1045	-0.1147	-0.0202	0.1031	-0.0583	0.002	0.1818	-0.1999	-0.1148	0.1161	0.2893	0.0565	-0.0365	0.2803	0.0034	0.2875	-24.7843	16.495	-10.0872
8	1.8418	-0.2238	0.0908	0.7135	-0.0918	1.183	-0.1673	-0.1733	-0.009	0.0278	0.0336	0.167	-0.1524	-0.1277	0.1217	0.2954	0.0508	-0.0335	0.2723	0.0009	0.2985	-24.1649	12.4798	-7.0965
9	0.7272	0.2206	-0.1022	1.2381	-0.1152	1.2295	-0.1584	0.0443	0.3079	-0.1135	0.0052	0.124	-0.5058	-0.0331	0.1361	0.4752	0.0153	-0.1268	0.2972	0.038	0.371	-18.232	31.3811	-21.5897
10	0.6758	-0.2828	0.2943	1.7283	-0.206	1.4226	-0.0379	0.2065	0.1606	-0.2854	-0.0969	-0.1529	-0.2163	0.345	0.1333	0.3891	-0.0311	-0.0288	0.3879	0.0904	0.2819	-5.685	20.5614	-34.0646
11	2.9876	0.4316	0.0013	1.9517	0.5885	4.7188	-0.1133	0.3235	0.1134	-0.0535	-0.049	0.2537	-0.2003	-0.6465	0.1779	0.5328	0.0417	-0.0992	0.5149	0.0269	0.3776	-24.8349	19.6819	-47.1091
12	0.7342	-0.1503	-0.2254	1.1749	0.2102	1.6427	-0.1407	-0.3052	0.3674	0.3167	0.1179	-0.1162	-0.5935	-0.0686	-0.108	0.5382	0.0997	-0.1076	0.3896	-0.1209	0.3785	-7.6996	26.8167	28.0214
13	0.773	-0.0175	0.1826	1.2574	-0.0796	1.2566	-0.1161	-0.2851	-0.1188	0.1926	0.1473	0.1401	0.01	-0.2552	-0.0296	0.25	0.0796	0.036	0.397	0.0262	0.2495	-15.494	-2.0024	24.9809
14	0.9631	0.1577	-0.0858	2.0097	-0.7333	1.6277	-0.1056	-0.1777	-0.0821	0.0235	0.1258	0.1618	-0.0261	-0.1764	-0.0033	0.2071	0.0505	0.0063	0.3986	0.011	0.2668	-15.9618	-3.1372	19.9711
15	0.9751	-0.195	-0.0011	1.1032	0.1929	1.1374	-0.1893	-0.3728	0.1499	0.4397	0.1491	0.0196	-0.3149	-0.1198	0.0195	0.5061	0.1724	-0.0142	0.4754	-0.0716	0.2928	-16.5795	18.9282	34.6859
16	1.3196	0.3227	-0.3236	1.4134	-0.3399	2.4602	-0.2726	-0.5603	0.2264	0.2703	0.1885	0.3419	-0.454	-0.6856	0.043	0.8477	0.367	-0.0145	0.8584	-0.1158	0.5407	-31.9604	28.3801	40.2628
17	1.5619	0.1049	-1.2052	1.5276	0.0216	2.2116	-0.0657	0.02	-0.1633	0.1869	-0.0223	0.3173	0.0213	-0.3539	0.1066	0.7558	0.251	0.0416	1.1175	-0.0675	0.6758	-40.2224	16.7683	43.813

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 63 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 64 through 303 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 304 through 463 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 464 through 526 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 527 through 677 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 10 through 108 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 109 through 245 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 246 through 297 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 298 through 406 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 407 through 555 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 556 through 677 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 11 through 108 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 109 through 245 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 246 through 297 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 298 through 526 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 527 through 579 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 580 through 677 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi