PDB-7mmz: Crystal Structure of Acetyl-coenzyme A synthetase from Legionella...

ID or keywords:

Entry

Database: PDB / ID: 7mmz

Title

Crystal Structure of Acetyl-coenzyme A synthetase from Legionella pneumophila Philadelphia 1 in complex with ethyl-AMP

Components

Acetyl-coenzyme A synthetase

Keywords

LIGASE / SSGCID / Acetyl-coenzyme A synthetase / ACS-1 / Legionella pneumophila / 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
Similarity search - Function

Biological species

Legionella pneumophila subsp. pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Bacterial structural genomics target enabled by a recently discovered potent fungal acetyl-CoA synthetase inhibitor.
Authors: DeBouver, N.D. / Bolejack, M.J. / Esan, T.E. / Krysan, D.J. / Hagen, T.J. / Abendroth, J.

History

Deposition	Apr 30, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 26, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jun 7, 2023	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7mmz.cif.gz	279.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7mmz.ent.gz	185.3 KB	Display	PDB format
PDBx/mmJSON format	7mmz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7mmz_validation.pdf.gz	797.3 KB	Display	wwPDB validaton report
Full document	7mmz_full_validation.pdf.gz	801 KB	Display
Data in XML	7mmz_validation.xml.gz	21.7 KB	Display
Data in CIF	7mmz_validation.cif.gz	30.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mm/7mmz ftp://data.pdbj.org/pub/pdb/validation_reports/mm/7mmz	HTTPS FTP

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Related structure data

Related structure data	1pg4S S: Starting model for refinement
Similar structure data	2ele-d 2e08-d 3pps-1 3ufg-d 2dsh-d 2gf6-2 2pb4-d 5hlj-1 1zj9-2 2p6k-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: LepnA.00629.a

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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

hetero molecules

71.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	74.930, 74.930, 228.790
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2
Space group name Hall	P4abw2nw
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+1/4 #3: y+1/2,-x+1/2,z+3/4 #4: x+1/2,-y+1/2,-z+3/4 #5: -x+1/2,y+1/2,-z+1/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

#1: Protein	Acetyl-coenzyme A synthetase Mass: 70631.477 Da / Num. of mol.: 1 / Fragment: LepnA.00629.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: acsB, lpg0127 / Plasmid: LepnA.00629.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZZ84, acetate-CoA ligase
#2: Chemical	ChemComp-WTA / 5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine Mass: 375.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₁₈N₅O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.28 Å³/Da / Density % sol: 46.06 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: RigakuReagents Wizard JCSG Top96 screen, condition B6: 100mM HEPES free acid / sodium hydroxide pH 7.5, 20% (w/V) PEG 4000, 20% (V/V) isopropanol: LepnA.00629.a.B1.PW38314 at 20mg/ml + 2mM ...Details: RigakuReagents Wizard JCSG Top96 screen, condition B6: 100mM HEPES free acid / sodium hydroxide pH 7.5, 20% (w/V) PEG 4000, 20% (V/V) isopropanol: LepnA.00629.a.B1.PW38314 at 20mg/ml + 2mM TCEP + 3mM ethylAMP (BSI111322): tray 319765 B6, cryo 20% EG + compound: puck hyq3-9.

Crystal

Density Matthews: 2.28 Å³/Da / Density % sol: 46.06 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: RigakuReagents Wizard JCSG Top96 screen, condition B6: 100mM HEPES free acid / sodium hydroxide pH 7.5, 20% (w/V) PEG 4000, 20% (V/V) isopropanol: LepnA.00629.a.B1.PW38314 at 20mg/ml + 2mM ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 11, 2021 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. obs: 26436 / % possible obs: 99.5 % / Redundancy: 7.846 % / B_iso Wilson estimate: 53.085 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.064 / R_rim(I) all: 0.069 / Χ²: 0.935 / Net I/σ(I): 20.74

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.4-2.46	8.156	0.618	4.42	1908	0.927	0.662	100
2.46-2.53	8.112	0.473	5.68	1874	0.949	0.508	99.9
2.53-2.6	8.111	0.39	6.54	1817	0.949	0.418	100
2.6-2.68	8.091	0.323	7.56	1767	0.958	0.347	99.8
2.68-2.77	8.061	0.246	9.4	1710	0.979	0.264	99.8
2.77-2.87	7.998	0.189	11.44	1660	0.988	0.203	99.8
2.87-2.98	7.932	0.148	13.98	1595	0.991	0.159	99.7
2.98-3.1	7.925	0.115	17.09	1555	0.993	0.124	99.7
3.1-3.24	7.904	0.093	20.48	1478	0.995	0.099	99.5
3.24-3.39	7.809	0.073	24.11	1428	0.997	0.079	99.4
3.39-3.58	7.757	0.062	28.18	1367	0.997	0.066	99.3
3.58-3.79	7.719	0.053	32.21	1290	0.998	0.057	99.5
3.79-4.06	7.696	0.047	36.35	1212	0.997	0.05	99.5
4.06-4.38	7.564	0.043	38.47	1155	0.997	0.046	99.1
4.38-4.8	7.626	0.04	39.47	1065	0.998	0.043	99.7
4.8-5.37	7.551	0.039	40.42	977	0.998	0.042	99.4
5.37-6.2	7.575	0.039	39.4	865	0.998	0.042	99.7
6.2-7.59	7.326	0.035	40.68	758	0.999	0.037	99.7
7.59-10.73	7.122	0.032	42.68	605	0.998	0.034	99.2
10.73-50	6.317	0.033	41.44	350	0.998	0.036	90.7

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19 dev 4205	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1pg4 as per Morda

1pg4

Resolution: 2.4→45.47 Å / SU ML: 0.2678 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.5599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2254	2041	7.74 %	0
R_work	0.1875	24321	-	-
obs	0.1904	26362	99.61 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 54.88 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→45.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4214	0	29	122	4365

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0056	4367
X-RAY DIFFRACTION	f_angle_d	0.7574	5981
X-RAY DIFFRACTION	f_chiral_restr	0.052	676
X-RAY DIFFRACTION	f_plane_restr	0.0069	779
X-RAY DIFFRACTION	f_dihedral_angle_d	14.6756	1509

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 (%)
2.4-2.46	0.2651	150	0.2434	1561	X-RAY DIFFRACTION	99.94
2.46-2.52	0.2739	133	0.2125	1590	X-RAY DIFFRACTION	99.94
2.52-2.59	0.2701	122	0.2104	1613	X-RAY DIFFRACTION	99.88
2.59-2.66	0.2427	142	0.212	1574	X-RAY DIFFRACTION	99.77
2.66-2.75	0.2799	137	0.2035	1581	X-RAY DIFFRACTION	99.83
2.75-2.85	0.2192	133	0.2245	1593	X-RAY DIFFRACTION	99.77
2.85-2.96	0.2618	120	0.2274	1610	X-RAY DIFFRACTION	99.71
2.96-3.09	0.2531	145	0.2265	1604	X-RAY DIFFRACTION	99.83
3.09-3.26	0.2974	111	0.2078	1636	X-RAY DIFFRACTION	99.37
3.26-3.46	0.2504	140	0.1961	1591	X-RAY DIFFRACTION	99.43
3.46-3.73	0.2248	153	0.1854	1612	X-RAY DIFFRACTION	99.27
3.73-4.1	0.214	136	0.1687	1623	X-RAY DIFFRACTION	99.49
4.1-4.69	0.203	134	0.1494	1654	X-RAY DIFFRACTION	99.44
4.7-5.91	0.1845	130	0.1595	1690	X-RAY DIFFRACTION	99.56
5.92-45.47	0.1962	155	0.1933	1789	X-RAY DIFFRACTION	99.03

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	3.33754437007	1.12568214192	0.91809156178	2.70757002661	0.580749807643	3.89297361142	-0.177245094102	-0.294532258811	0.456553074003	0.239765981998	-0.00763507243159	0.668808835042	-0.096698524512	-0.474205134844	0.22093303286	0.37173744259	0.00581859824973	0.109716328285	0.368868461322	-0.0721190872537	0.667815848833	-29.4086490143	30.7991064803	28.6413355481
2	3.02642866649	0.101628526066	-0.355516884039	2.58128455992	0.407278252668	1.49532269261	-0.543202331715	0.834136490571	0.020154829102	-0.619718750231	0.408243852654	0.297479509445	0.0737809158401	-0.152252860014	0.126251205116	0.613834995263	-0.284028877671	-0.0243533264215	0.479036175268	0.0293146906151	0.35537610875	-19.9951987591	23.0329358358	5.39796073012
3	2.07138150085	0.0476740912359	0.199976034302	1.80702796788	0.11135144007	1.90145401909	-0.863711300101	1.25882228005	-0.595450848812	-0.927107734071	0.764051844831	-0.207849629311	0.560874748771	-0.0799406032309	-0.0557060860946	0.96216202527	-0.466759147974	0.16906228988	0.757869599897	-0.198553860237	0.530833491888	-15.2715074288	11.8412991251	-1.40858600684
4	2.96695045909	0.537951930171	0.0369834838395	2.62475719384	0.572631478455	1.891198036	-0.239162274386	0.111638221379	-0.0622291176586	-0.0283132336584	0.0521254266659	0.452213796528	0.199769025811	-0.26916625663	0.112950053193	0.427579953524	-0.103156210515	0.0413780870736	0.265424436005	-0.0103554639459	0.368934032225	-21.9593504712	23.2811618426	18.9871031183
5	2.80925126276	1.20771920052	-0.464014849102	2.77834426155	0.132030461758	1.80696550808	-0.553684095651	0.595574376321	0.282874450117	-0.659529070552	0.435285738391	-0.143047645263	-0.279594791651	0.134068721821	0.0694138396249	0.526960692427	-0.19718462534	0.0076455326412	0.332443543562	0.0492745345611	0.381067095826	-3.66354088522	36.6786625825	10.8021824001
6	2.94476514063	2.58214184075	-0.697859290927	3.913754593	0.617571628419	1.48388205439	0.0241016709645	-0.0236790808712	0.637084760524	0.285159206432	-0.00561042706462	0.331339873329	-0.100367790618	0.197423578727	0.0939061561545	0.456228017828	-0.0468367414077	-0.00729388244493	0.290902203159	-0.00601759851091	0.437021616272	-7.41751206736	37.464995463	26.0967679374
7	4.46678987368	1.2103169093	-0.213517915864	3.24305862258	0.485653151495	2.27983348074	-0.15913450628	-0.371211018964	-0.393757347917	0.554888060961	0.0550580784134	-0.245389034005	0.434896329962	0.236227055825	0.0543424686575	0.53123469431	0.0262729495058	0.0116715863721	0.275139759215	0.0323482564079	0.307647489448	-6.44672699461	22.3056677261	32.0055664418
8	2.51090235689	-3.87609942677	-0.457305127889	6.15255384677	1.15938121238	4.78154645475	-0.372659704224	0.878350030014	-1.20470641667	-0.216127200898	0.810522417284	-1.75904970386	-0.0521963671036	1.04840364668	-0.173821163486	0.515269798671	0.0246315772543	0.214960049251	0.622042975952	-0.296521175829	1.2543091541	9.58469585258	10.0479871182	17.121416998

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 12 through 63 )	12 - 63	1 - 52
2	2	chain 'A' and (resid 64 through 160 )	64 - 160	53 - 149
3	3	chain 'A' and (resid 161 through 221 )	161 - 221	150 - 210
4	4	chain 'A' and (resid 222 through 270 )	222 - 270	211 - 259
5	5	chain 'A' and (resid 271 through 385 )	271 - 385	260 - 374
6	6	chain 'A' and (resid 386 through 416 )	386 - 416	375 - 405
7	7	chain 'A' and (resid 417 through 528 )	417 - 528	406 - 517
8	8	chain 'A' and (resid 529 through 575 )	529 - 575	518 - 559

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