PDB-6arf: Aspergillus fumigatus Cytosolic Thiolase: Apo enzyme in complex w...

ID or keywords:

Entry

Database: PDB / ID: 6arf

Title

Aspergillus fumigatus Cytosolic Thiolase: Apo enzyme in complex with potassium ions

Components

Acetyl-CoA acetyltransferase

Keywords

TRANSFERASE / thiolase / Claisen Condensation / monovalent cation binding

Function / homology

Function and homology information

ergosterol biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / fatty acid beta-oxidation / mitochondrion / metal ion binding / cytosol
Similarity search - Function

Biological species

Neosartorya fumigata (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.702 Å

Authors

Marshall, A.C. / Bond, C.S. / Bruning, J.B.

Citation

Journal: Acs Catalysis / Year: 2018
Title: Structure of Aspergillus fumigatus Cytosolic Thiolase: Trapped Tetrahedral Reaction Intermediates and Activation by Monovalent Cations
Authors: Marshall, A.C. / Bond, C.S. / Bruning, J.B.

History

Deposition	Aug 22, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 30, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6arf.cif.gz	620.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6arf.ent.gz	510.6 KB	Display	PDB format
PDBx/mmJSON format	6arf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6arf_validation.pdf.gz	7.5 MB	Display	wwPDB validaton report
Full document	6arf_full_validation.pdf.gz	7.5 MB	Display
Data in XML	6arf_validation.xml.gz	71.6 KB	Display
Data in CIF	6arf_validation.cif.gz	107.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ar/6arf ftp://data.pdbj.org/pub/pdb/validation_reports/ar/6arf	HTTPS FTP

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Related structure data

Related structure data	6aqpC 6areC 6argC 6arlC 6arrC 6artC C: citing same article (ref.)
Similar structure data	1m1t-d 6art-d 1m4s-d 6arg-d 2wl6-d 6aqp-d 2vu0-d 4o9a-d 6l2c-d 4o9c-1 1m3k-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#216 - Dec 2017 Biodegradable Plastic similarity (11) #90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

A: Acetyl-CoA acetyltransferase

B: Acetyl-CoA acetyltransferase

C: Acetyl-CoA acetyltransferase

D: Acetyl-CoA acetyltransferase

hetero molecules

165 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	71.440, 105.410, 110.420
Angle α, β, γ (deg.)	90.000, 108.740, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Acetyl-CoA acetyltransferase Mass: 41007.848 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold) Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_8G04000 / Plasmid: pET-57-DEST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4WCL5, acetyl-CoA C-acetyltransferase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1569 / Source method: isolated from a natural source / Formula: H₂O

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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: 49.03 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion / Details: 20% PEG 3350, 0.2M KCl, 0.2M KF

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX1 / Wavelength: 0.9537 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2017

Radiation

Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9537 Å / Relative weight: 1

Reflection

Resolution: 1.7→36.26 Å / Num. obs: 169059 / % possible obs: 99.9 % / Redundancy: 6.5 % / B_iso Wilson estimate: 20.42 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.133 / R_pim(I) all: 0.056 / R_rim(I) all: 0.144 / Net I/σ(I): 9.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
1.7-1.73	5.7	1.819	8191	0.329	0.83	2.006	99
9.32-36.26	6.4	0.03	1060	0.999	0.013	0.033	97.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	8.18 Å	41.55 Å
Translation	8.18 Å	41.55 Å

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Processing

Software

Name	Version	Classification
MOSFLM		data collection
Aimless	0.5.17	data scaling
PHASER	2.5.7	phasing
PHENIX	dev_2686	refinement
PDB_EXTRACT	3.22	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.702→36.255 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.02

	R_factor	Num. reflection	% reflection
R_free	0.2	8517	5.04 %
R_work	0.1653	-	-
obs	0.1671	168972	99.86 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 130.41 Å² / B_iso mean: 41.4296 Å² / B_iso min: 8.41 Å²

Refinement step

Cycle: final / Resolution: 1.702→36.255 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11334	0	47	1569	12950
B_iso mean	-	-	43.13	42.9	-
Num. residues	-	-	-	-	1583

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	11678
X-RAY DIFFRACTION	f_angle_d	0.809	15878
X-RAY DIFFRACTION	f_chiral_restr	0.055	1880
X-RAY DIFFRACTION	f_plane_restr	0.006	2096
X-RAY DIFFRACTION	f_dihedral_angle_d	15.146	7138

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.702-1.7213	0.3426	271	0.3171	5200	5471	98
1.7213-1.7416	0.3387	281	0.3089	5341	5622	100
1.7416-1.7628	0.3336	271	0.2952	5311	5582	100
1.7628-1.7852	0.2892	272	0.2694	5383	5655	100
1.7852-1.8086	0.2952	280	0.2718	5284	5564	100
1.8086-1.8334	0.2874	307	0.2555	5341	5648	100
1.8334-1.8596	0.2731	301	0.2449	5276	5577	100
1.8596-1.8874	0.2626	261	0.2347	5406	5667	100
1.8874-1.9169	0.26	316	0.2392	5292	5608	100
1.9169-1.9483	0.2854	254	0.2406	5336	5590	100
1.9483-1.9819	0.245	287	0.2157	5377	5664	100
1.9819-2.0179	0.2341	247	0.2054	5362	5609	100
2.0179-2.0567	0.2378	299	0.1988	5340	5639	100
2.0567-2.0987	0.2525	254	0.1885	5325	5579	100
2.0987-2.1443	0.2067	296	0.1745	5347	5643	100
2.1443-2.1942	0.2189	286	0.174	5338	5624	100
2.1942-2.2491	0.2085	280	0.1751	5408	5688	100
2.2491-2.3099	0.2071	283	0.1718	5344	5627	100
2.3099-2.3778	0.1995	264	0.1679	5344	5608	100
2.3778-2.4545	0.2055	312	0.1605	5337	5649	100
2.4545-2.5423	0.1997	299	0.1614	5339	5638	100
2.5423-2.644	0.195	251	0.1597	5405	5656	100
2.644-2.7643	0.1975	265	0.1565	5364	5629	100
2.7643-2.91	0.1886	307	0.1528	5332	5639	100
2.91-3.0922	0.1928	316	0.1541	5341	5657	100
3.0922-3.3308	0.1879	282	0.1444	5367	5649	100
3.3308-3.6657	0.1801	265	0.1419	5394	5659	100
3.6657-4.1955	0.1515	314	0.1184	5349	5663	100
4.1955-5.2833	0.1437	299	0.1131	5424	5723	100
5.2833-36.2636	0.1615	297	0.1319	5448	5745	100

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	1.6994	-0.3165	-0.14	1.2387	-0.1424	1.197	-0.2401	0.0599	-0.3784	0.3163	-0.0437	0.5665	0.2035	-0.5531	0.2213	0.3531	-0.0455	0.1665	0.6126	0.0067	0.3748	-44.4279	16.9147	157.9558
2	2.7007	-0.3401	0.0002	3.2833	-0.0399	1.449	-0.1289	0.7134	-0.3357	-0.2959	0.1875	0.5858	0.1125	-0.5309	-0.1128	0.3365	-0.1282	0.0953	1.0601	-0.2374	0.8363	-56.5665	14.6045	146.5626
3	1.6215	0.1475	-0.2322	0.28	-0.3963	0.5602	-0.2778	-0.1518	-0.8426	0.5179	0.0493	0.6881	0.5454	-0.9143	0.2169	0.685	-0.2	0.4126	0.893	-0.0082	0.7652	-52.8909	7.6059	166.7241
4	1.5886	-0.5489	0.4779	1.069	0.0746	2.5547	-0.248	-0.1524	-0.0087	0.4352	0.0464	-0.123	0.0661	0.3059	0.1913	0.3973	0.0224	0.009	0.4824	0.0813	0.169	-22.6268	19.3039	164.3086
5	2.2506	-0.0837	0.5652	0.9249	0.0281	1.4564	-0.3771	-0.4921	0.5746	0.7615	0.1297	-0.1153	-0.1986	0.3624	0.2625	0.7002	0.094	-0.1061	0.717	0.0655	0.1494	-19.8168	27.4266	174.713
6	2.7743	-1.1606	-0.6563	0.5654	0.526	4.2736	0.11	0.0447	0.095	-0.047	0.0644	0.1474	-0.3459	-0.0353	-0.2298	0.1359	-0.0344	-0.0372	0.0325	-0.0012	0.188	-37.854	28.2742	105.7219
7	1.539	-0.0373	0.2277	0.7616	-0.3388	0.529	-0.0548	-0.153	0.1347	0.0602	0.0646	0.1446	-0.0984	-0.0766	-0.011	0.125	0.0196	-0.0066	0.0834	-0.0051	0.1644	-32.1197	31.1839	113.9109
8	2.0077	-0.3321	0.0628	1.1746	-0.0937	0.8457	-0.0447	-0.0068	0.3279	0.0053	0.0658	0.1809	-0.1235	-0.0891	-0.0326	0.151	0.0234	-0.0234	0.0903	0.0221	0.2556	-40.0303	38.7635	106.2955
9	2.3742	-0.5101	-0.1462	2.5193	-1.0904	0.6867	-0.1351	0.0616	0.2515	-0.0463	0.0076	-0.2015	0.0883	0.0086	0.0702	0.0913	-0.0401	-0.019	0.1214	-0.0198	0.1474	-6.1077	29.9397	113.0687
10	1.6331	-0.2169	0.161	0.5597	-0.173	0.7048	-0.0686	-0.1421	0.0044	0.0607	0.0374	-0.0421	0.0002	0.0566	0.0319	0.1182	0.0124	-0.0026	0.1038	-0.0135	0.1165	-14.3475	24.7531	116.5078
11	2.8137	0.6466	-0.4826	3.9239	-1.2174	4.1729	-0.0385	-0.6124	0.4008	0.4682	-0.0321	-0.2582	-0.4368	0.1547	-0.0064	0.184	0.0014	-0.0887	0.2868	-0.0742	0.2429	3.2054	30.4741	123.98
12	1.7484	-0.3782	0.2628	1.1766	-0.1986	0.8184	-0.0265	0.0773	-0.1582	-0.0545	-0.0031	-0.1294	0.0917	0.152	0.0398	0.1038	0.0116	0.0119	0.1144	-0.0104	0.152	-4.5431	17.9854	108.3943

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 196 )	A	4 - 196
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 197 through 256 )	A	197 - 256
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 257 through 398 )	A	257 - 398
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 0 through 224 )	B	0 - 224
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 225 through 398 )	B	225 - 398
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 1 through 28 )	C	1 - 28
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 29 through 195 )	C	29 - 195
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 196 through 398 )	C	196 - 398
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 1 through 28 )	D	1 - 28
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 29 through 195 )	D	29 - 195
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 196 through 224 )	D	196 - 224
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 225 through 398 )	D	225 - 398

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