PDB-7kq6: Crystal Structure of Acetyl-coenzyme A synthetase from Coccidioid...

ID or keywords:

Entry

Database: PDB / ID: 7kq6

Title

Crystal Structure of Acetyl-coenzyme A synthetase from Coccidioides immitis in complex with PRX

Components

Acetyl-coenzyme A synthetase

Keywords

LIGASE / SSGCID / Acetyl-coenzyme A synthetase / PRX / 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

Coccidioides immitis (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Acetyl-coenzyme A synthetase synthetase from Coccidioides immitis in complex with PRX
Authors: DeBouver, N.D. / Fox III, D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Nov 13, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 9, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7kq6.cif.gz	896.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7kq6.ent.gz	608.6 KB	Display	PDB format
PDBx/mmJSON format	7kq6.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/kq/7kq6 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/7kq6	HTTPS FTP

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Related structure data

Related structure data	7l9tC 7kcpS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7l3q-1 7l3q-2 7kqz-d 7l4g-3 7kvy-d 5e4t-d 7l3p-d 2x8b-d 4k4u-1 6b58-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

7l9tC

7kcpS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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

238 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
79.4 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
79.6 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
79.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	106.980, 116.080, 107.330
Angle α, β, γ (deg.)	90.000, 119.755, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Acetyl-coenzyme A synthetase Mass: 78435.828 Da / Num. of mol.: 3 / Fragment: LepnA.00116.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coccidioides immitis (strain RS) (fungus) Strain: RS / Gene: CIMG_01510 / Plasmid: CoimA.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J3KJC6, acetate-CoA ligase
#2: Chemical	ChemComp-PRX / ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / ADENOSINE-5'-PROPYLPHOSPHATE Mass: 389.301 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₃H₂₀N₅O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1554 / 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: 2.46 Å³/Da / Density % sol: 49.97 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: CoimA.00629.a.FS11.PD00400 [Barcode: 313284h5, PuckID: ejj3-8, Cryo: 20% EG, Concentration: 10 mg/mL] 200 mM Potassium chloride, 20% (w/v) PEG 3350

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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: Nov 14, 2019 / 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: 1.8→50 Å / Num. obs: 201793 / % possible obs: 95.8 % / Redundancy: 3.066 % / B_iso Wilson estimate: 31.077 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.048 / R_rim(I) all: 0.057 / Χ²: 0.931 / Net I/σ(I): 15.73

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
1.8-1.85	2.989	0.545	2.1	15201	0.744	0.656	97.9
1.85-1.9	3.001	0.433	2.67	14767	0.822	0.521	97.8
1.9-1.95	3.015	0.334	3.47	14436	0.883	0.402	97.4
1.95-2.01	3.025	0.27	4.32	13826	0.923	0.324	97.2
2.01-2.08	3.033	0.218	5.42	13461	0.948	0.262	97
2.08-2.15	3.044	0.167	7.12	12953	0.969	0.2	96.8
2.15-2.23	3.051	0.134	8.7	12521	0.98	0.161	96.5
2.23-2.32	3.061	0.106	10.78	12047	0.987	0.127	96.3
2.32-2.43	3.071	0.085	13.26	11400	0.991	0.102	96
2.43-2.55	3.084	0.073	15.43	10973	0.993	0.087	95.8
2.55-2.68	3.088	0.062	17.84	10425	0.995	0.073	95.7
2.68-2.85	3.094	0.051	21.21	9765	0.997	0.061	95.4
2.85-3.04	3.099	0.041	25.93	9220	0.998	0.049	94.9
3.04-3.29	3.105	0.034	30.13	8478	0.998	0.04	94.3
3.29-3.6	3.115	0.028	36.19	7839	0.999	0.033	93.9
3.6-4.02	3.132	0.024	41.22	6977	0.999	0.028	93
4.02-4.65	3.16	0.021	44.96	6213	0.999	0.025	92.5
4.65-5.69	3.19	0.02	46.03	5162	0.999	0.023	92.2
5.69-8.05	3.235	0.019	46.25	3991	0.999	0.023	91.2
8.05-50	3.185	0.017	50.8	2138	0.999	0.02	86.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	4.82 Å	46.59 Å
Translation	4.82 Å	46.59 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.19rc4-4035	refinement
XDS		data reduction
XSCALE		data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7KCP

7kcp

Resolution: 1.8→46.59 Å / SU ML: 0.2149 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8927
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1846	2010	1 %
R_work	0.1616	199764	-
obs	0.1618	201774	95.99 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.1 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→46.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13963	0	206	1554	15723

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0066	14656
X-RAY DIFFRACTION	f_angle_d	0.7909	19952
X-RAY DIFFRACTION	f_chiral_restr	0.0569	2169
X-RAY DIFFRACTION	f_plane_restr	0.0069	2605
X-RAY DIFFRACTION	f_dihedral_angle_d	11.9851	5194

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 (%)
1.8-1.85	0.3186	147	0.2594	14524	X-RAY DIFFRACTION	97.94
1.85-1.89	0.2828	149	0.2319	14469	X-RAY DIFFRACTION	97.91
1.89-1.95	0.2448	148	0.2047	14501	X-RAY DIFFRACTION	97.56
1.95-2.01	0.2566	142	0.1936	14382	X-RAY DIFFRACTION	97.32
2.01-2.09	0.2346	138	0.1885	14405	X-RAY DIFFRACTION	97.09
2.09-2.17	0.2268	142	0.1756	14371	X-RAY DIFFRACTION	96.82
2.17-2.27	0.211	146	0.159	14316	X-RAY DIFFRACTION	96.7
2.27-2.39	0.184	141	0.1515	14311	X-RAY DIFFRACTION	96.24
2.39-2.54	0.1606	145	0.152	14208	X-RAY DIFFRACTION	95.93
2.54-2.73	0.1843	140	0.1598	14273	X-RAY DIFFRACTION	95.82
2.73-3.01	0.1783	140	0.1561	14188	X-RAY DIFFRACTION	95.39
3.01-3.44	0.1724	146	0.1547	14075	X-RAY DIFFRACTION	94.45
3.44-4.34	0.1652	137	0.1362	13914	X-RAY DIFFRACTION	93.32
4.34-46.59	0.1507	149	0.1561	13827	X-RAY DIFFRACTION	91.55

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	1.0134184699	-0.340445104831	0.454241167439	1.34624932345	-0.110873648597	2.0910434974	0.0200966561739	0.0983369439218	-0.228302560636	0.0562449718319	-0.0510351179233	-0.37812455067	0.289070750325	0.484590228664	0.0413545453768	0.280064028203	0.0973975047759	-0.00280339371907	0.327778438584	0.0121576001926	0.423067146461	40.0455470758	-18.1462936517	36.0879034549
2	0.64516361746	-0.00598270784276	0.191045521181	0.682096659245	0.286455519105	0.946663278503	-0.0182643340775	-0.00930884277518	0.0627551970841	-0.0422420432074	-0.00661084489956	-0.00407266916969	-0.127288458706	0.0782236751755	0.0189120687724	0.154270918988	-0.0208017566245	-0.00453802169972	0.115404855307	0.00687370908265	0.16785141708	16.6416942299	7.24979487625	42.3699389895
3	0.957258085631	-0.0140361061836	0.361653215983	0.464479921728	0.0484676278972	1.0484974707	0.00654845480322	0.0528367963687	-0.0353333160067	-0.00274991147088	-0.0222343422205	-0.125023442433	0.0132770507626	0.259488351308	0.0145107652989	0.168263994138	-0.000680716939018	0.00423718674144	0.194253968117	0.02333775657	0.202402892362	35.6565234947	-3.03345619953	40.3513890601
4	3.51533648799	-1.2882825258	0.810284671334	2.03506267984	-0.880457780468	1.83153026656	-0.0255651995287	0.285607984997	0.153099775809	-0.0714717814533	-0.0857642007502	-0.286370594476	-0.0172661759125	0.41271281187	0.103864670782	0.207438028966	-0.020620107792	0.018434788324	0.262900138824	0.00161324287491	0.176316697986	34.6757056748	1.02146448487	22.8773743996
5	5.09431159608	2.45156833502	0.249725718696	2.10004488918	1.88287367163	3.23015603756	0.224834128073	-0.268309261281	0.355211589351	0.340803521225	-0.58584745191	-0.882956305685	-0.0314972973233	0.230234007859	0.265100472997	0.497034859503	-0.203499701205	-0.0808960792596	0.533909566582	0.156076341146	0.608170167186	44.3574472098	23.5009537645	30.6931709214
6	6.68718807824	3.62818904449	-0.495970111029	2.49318236171	0.0146851528549	0.211976430302	0.452239417134	-0.269287025751	0.216529594624	0.822064986288	-0.693296665378	-0.810587757293	-0.681181396875	0.629653281716	0.020867725969	0.582474325086	-0.279263337073	-0.148102896775	0.531679332273	0.187318561295	0.789619400389	43.8019933477	27.2478796711	35.8154593704
7	0.981565025726	0.264094432338	-0.16678541933	0.887758378892	-0.145405416394	0.690010156716	0.0141292394971	0.139951446682	0.0500578424886	-0.0407795399295	-0.00551128152505	0.0646339339953	-0.0384096409621	-0.0137726241176	0.00861489402679	0.168699068123	0.00708581904713	-0.0042635375309	0.138798776242	0.00979213788671	0.120292146196	-1.45670997837	2.20346291911	8.24100493316
8	0.877538507285	0.131452280529	-0.0850243783695	0.443853016787	0.0426816116149	0.797206456251	-0.0226769000941	0.265464941446	0.00427848823752	-0.0921939237013	-0.00321495036742	0.0837076959842	0.00461303834979	-0.106413154977	0.0217298414594	0.174917307661	0.000641701074193	-0.0112467922961	0.193601879183	-0.00390874674545	0.144278741981	-11.8175236699	-3.38035432307	-1.55894738794
9	1.09947262864	0.203874037826	-0.212294465079	2.21743534403	-0.51406751728	0.905278163492	-0.0300019892863	0.312802069361	0.653510783337	-0.360805809918	-0.0905806116196	0.553860821485	-0.419353863109	-0.235493162631	0.0699924860977	0.495905318094	0.0903215483148	-0.117564341642	0.42716918777	0.102229937542	0.581419339589	-21.8274358655	14.8590490984	-6.052462234
10	1.50307046123	-0.221746164392	0.857446807091	0.920794162882	0.0417141801603	1.28580396412	0.116705595997	-0.363223591231	-0.18942811976	0.0764646426327	-0.018360776093	0.0585073965549	0.211073457112	-0.34894339748	-0.00510744798789	0.166695226487	-0.0646019849953	0.0254374418573	0.229743062997	0.0357431120455	0.161916737331	-17.6770434441	-6.89880748841	46.2902653661
11	1.2816961792	-0.664128361431	0.313568557614	1.38575522355	0.221836332823	1.17610172811	-0.152826510857	-0.244882842645	0.365800679665	0.0423510579777	0.028929261873	-0.0408515727475	-0.216878693387	-0.22355436101	0.0779529513443	0.20269883747	0.0526294623316	-0.0092878709767	0.199654023115	-0.0713353500057	0.276367612697	-21.0120831949	17.2839795179	39.9381629447
12	1.43636906816	-0.28528629996	0.770141839888	0.604402915789	-0.139925277674	1.20771710463	0.0994245967139	-0.664739803248	-0.109618874664	0.134384828062	0.010911422948	0.136083944235	0.102608461166	-0.63651205451	-0.0182453010622	0.192100267633	-0.0790891119039	0.036850377679	0.515158413746	0.039258680279	0.197148070247	-27.7908635816	-4.03036566508	54.9741063763
13	1.41343834008	-0.264855948361	-1.5637392162	2.83184992338	-1.35190643157	2.78847638896	0.192724185584	-0.77140285659	-0.0360261833057	0.645242865135	-0.0455676715946	-0.185131794267	0.175860858221	-0.0661813236792	-0.089109265673	0.305921150392	-0.0635373454975	-0.0482908280158	0.506546854399	0.065900043334	0.198444231342	-9.94428130558	-8.33653810188	71.9451829134
14	2.32159067273	1.1030435853	-0.665018705533	2.29099453135	-0.555159766884	2.20555661768	0.16228229163	-0.568283789362	0.0115736928949	0.317966932791	-0.137947333408	0.0864216117156	-0.048160461186	-0.309162444303	-0.0740824665566	0.195225365242	-0.0288188982493	-0.00095170844504	0.366302041155	-0.0161357112131	0.167141569731	-9.93686206238	0.0270720053602	65.3278835505
15	2.89672224249	-1.15870108731	-0.583038807025	0.462110878531	0.418413586757	3.81456746898	0.480918157231	0.0200811576345	0.182174839059	0.632338239452	-0.494874845627	0.580589326914	0.047033937386	-0.0640664092207	0.0186382373223	0.746132763837	0.14031489833	0.11174796311	0.878356714066	-0.306987095486	0.597144304888	-22.2583046027	22.2160993223	69.9641611859
16	0.618924173602	-0.666203224541	-1.87053606494	0.732595146244	2.04105171471	5.69672411789	-0.214340605011	-0.531255580658	0.414516649033	0.870847745705	-0.439294506363	1.24434473014	0.100460849778	-0.654070790535	0.520157993549	0.719077373255	0.137660560477	0.0941335330022	0.760125178235	-0.396470752059	0.781170637988	-26.7082663755	26.3858689828	66.5962027065

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 10 through 53 )	A	A	10 - 53	1 - 44
2	2	chain 'A' and (resid 54 through 270 )	A	A	54 - 270	45 - 261
3	3	chain 'A' and (resid 271 through 484 )	A	A	271 - 484	262 - 475
4	4	chain 'A' and (resid 485 through 542 )	A	A	485 - 542	476 - 533
5	5	chain 'A' and (resid 543 through 589 )	A	A	543 - 589	534 - 580
6	6	chain 'A' and (resid 590 through 619 )	A	A	590 - 619	581 - 610
7	7	chain 'B' and (resid 11 through 270 )	B	L	11 - 270	1 - 260
8	8	chain 'B' and (resid 271 through 517 )	B	L	271 - 517	261 - 507
9	9	chain 'B' and (resid 518 through 616 )	B	L	518 - 616	508 - 590
10	10	chain 'C' and (resid 11 through 174 )	C	Z	11 - 174	1 - 164
11	11	chain 'C' and (resid 175 through 270 )	C	Z	175 - 270	165 - 260
12	12	chain 'C' and (resid 271 through 454 )	C	Z	271 - 454	261 - 444
13	13	chain 'C' and (resid 455 through 484 )	C	Z	455 - 484	445 - 474
14	14	chain 'C' and (resid 485 through 542 )	C	Z	485 - 542	475 - 532
15	15	chain 'C' and (resid 543 through 589 )	C	Z	543 - 589	533 - 579
16	16	chain 'C' and (resid 590 through 618 )	C	Z	590 - 618	580 - 608

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