PDB-5wx3: Alkyldiketide-CoA synthase from Evodia rutaecarpa

ID or keywords:

Entry

Database: PDB / ID: 5wx3

Title

Alkyldiketide-CoA synthase from Evodia rutaecarpa

Components

Alkyldiketide-CoA synthase

Keywords

TRANSFERASE / polyketidesynthase

Function / homology

Function and homology information

polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function

Biological species

Tetradium ruticarpum (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.801 Å

Authors

Matsui, T. / Kodama, T. / Tadakoshi, T. / Morita, H.

Citation

Journal: J. Biol. Chem. / Year: 2017
Title: 2-Alkylquinolone alkaloid biosynthesis in the medicinal plant Evodia rutaecarpa involves collaboration of two novel type III polyketide synthases
Authors: Matsui, T. / Kodama, T. / Mori, T. / Tadakoshi, T. / Noguchi, H. / Abe, I. / Morita, H.

History

Deposition	Jan 6, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 26, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jun 14, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Nov 22, 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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PDBx/mmCIF format	5wx3.cif.gz	582 KB	Display	PDBx/mmCIF format
PDB format	pdb5wx3.ent.gz	480.9 KB	Display	PDB format
PDBx/mmJSON format	5wx3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5wx3_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5wx3_full_validation.pdf.gz	1.5 MB	Display
Data in XML	5wx3_validation.xml.gz	58.3 KB	Display
Data in CIF	5wx3_validation.cif.gz	79.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wx/5wx3 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/5wx3	HTTPS FTP

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Related structure data

Related structure data	5wx4C 5wx5C 5wx6C 5wx7C 3wd7S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6l7j-1 6cqb-d 3a5s-d 3eut-2 5aeg-1 4ku3-d 5ohs-8 5aed-2 5ohs-5 2h84-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#216 - Dec 2017 Biodegradable Plastic similarity (2) #90 - Jun 2007 Fatty Acid Synthase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Alkyldiketide-CoA synthase

B: Alkyldiketide-CoA synthase

C: Alkyldiketide-CoA synthase

D: Alkyldiketide-CoA synthase

hetero molecules

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

1

A: Alkyldiketide-CoA synthase

C: Alkyldiketide-CoA synthase

hetero molecules

defined by author&software
90 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Alkyldiketide-CoA synthase

D: Alkyldiketide-CoA synthase

hetero molecules

defined by author&software
90 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	164.590, 84.120, 138.670
Angle α, β, γ (deg.)	90.000, 124.740, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Alkyldiketide-CoA synthase Mass: 44156.855 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetradium ruticarpum (plant) / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: A0A1W7GKH6*PLUS
#2: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	the sequence database references for this protein does not currently exist in the UniProt database. ...the sequence database references for this protein does not currently exist in the UniProt database. this sequence has already been deposited to GenBank as LC208543. residues from MET (-11) to SER 0 are expression tags.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.1 M Bis-Tris, 0.2 M Ammonium sulfate, 25%(w/v) PEG3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: AR-NW12A / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 24, 2016

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection twin

Operator: h,-k,-h-l / Fraction: 0.04

Reflection

Resolution: 1.8→47.484 Å / Num. obs: 142923 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.051 / Net I/σ(I): 17.37

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	CC_1/2	Diffraction-ID	% possible all
1.8-1.91	0.477	2.8	0.848	1	97.8
1.91-2.04	0.274	4.97	0.942	1	99.6
2.04-2.2	0.168	8.02	0.977	1	99.6
2.2-2.41	0.109	12.08	0.989	1	99.6
2.41-2.7	0.072	17.36	0.994	1	99.6
2.7-3.11	0.045	25.3	0.998	1	99.7
3.11-3.81	0.028	38.76	0.999	1	99.5
3.81-5.37	0.022	49.17	0.999	1	99.5
5.37-47.484	0.023	51.03	0.999	1	98

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R rigid body: 0.573

	Highest resolution	Lowest resolution
Rotation	39.74 Å	2.02 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
MOLREP		phasing
PHENIX	(1.10.1_2155: ???)	refinement
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3WD7

3wd7

Resolution: 1.801→39.737 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.59

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2257	7290	5.1 %	Random
R_work	0.1918	-	-	-
obs	0.1937	142922	99.47 %	-

Solvent computation

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

Displacement parameters

B_iso max: 97.2 Å² / B_iso mean: 29.6887 Å² / B_iso min: 10.24 Å²

Refinement step

Cycle: final / Resolution: 1.801→39.737 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11385	0	212	454	12051
B_iso mean	-	-	56.34	25.7	-
Num. residues	-	-	-	-	1461

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	11872
X-RAY DIFFRACTION	f_angle_d	0.899	16099
X-RAY DIFFRACTION	f_chiral_restr	0.054	1777
X-RAY DIFFRACTION	f_plane_restr	0.005	2039
X-RAY DIFFRACTION	f_dihedral_angle_d	16.17	7070

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.801-1.8321	0.3746	336	0.3382	6379	6715	90
1.8321-1.8654	0.3164	358	0.297	6801	7159	95
1.8654-1.9013	0.3008	356	0.2757	6758	7114	95
1.9013-1.9401	0.2891	355	0.2559	6741	7096	95
1.9401-1.9822	0.2522	359	0.2331	6818	7177	95
1.9822-2.0284	0.2587	355	0.229	6758	7113	95
2.0284-2.0791	0.2376	356	0.2202	6754	7110	95
2.0791-2.1353	0.2624	360	0.2085	6845	7205	95
2.1353-2.1981	0.234	357	0.2032	6791	7148	95
2.1981-2.2691	0.2249	356	0.1972	6761	7117	95
2.2691-2.3501	0.2461	359	0.2024	6810	7169	95
2.3501-2.4442	0.2504	356	0.1955	6768	7124	95
2.4442-2.5554	0.2473	359	0.1992	6826	7185	95
2.5554-2.6901	0.2662	359	0.1973	6814	7173	95
2.6901-2.8586	0.2386	357	0.2013	6796	7153	95
2.8586-3.0793	0.2219	361	0.1974	6845	7206	95
3.0793-3.389	0.2125	359	0.189	6833	7192	95
3.389-3.879	0.2041	360	0.1618	6842	7202	95
3.879-4.8857	0.169	363	0.1343	6891	7254	95
4.8857-39.1743	0.1927	366	0.1784	6943	7309	94

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	0.6926	0.0474	0.0129	0.4944	0.2506	1.0474	-0.0622	0.1258	0.1503	-0.0228	0.0068	0.0709	-0.2525	0.0344	0.0337	0.2027	-0.022	-0.0274	0.1114	0.0329	0.1854	-7.536	6.1554	29.0249
2	1.1349	0.4002	-0.0058	1.4153	0.0373	1.2457	-0.0447	-0.1319	0.2299	0.1886	0.03	0.0939	-0.1911	-0.0653	0.0036	0.1966	0.0317	-0.0068	0.1104	-0.0284	0.1856	-18.5463	5.0921	46.553
3	8.0312	-2.5468	-5.0538	1.9146	1.8268	5.1736	-0.152	0.1068	0.1373	0.0797	0.0381	0.0872	-0.0292	-0.0452	0.1062	0.1647	-0.0213	-0.0301	0.0536	0.0116	0.1253	-10.0207	2.0459	35.371
4	1.7759	0.4104	-1.9019	1.615	0.7035	3.3967	-0.1493	0.095	0.3484	-0.0112	0.1704	-0.1449	0.1339	0.051	-0.0646	0.1469	-0.0092	-0.035	0.1186	0.0023	0.144	-10.3793	-0.7508	29.419
5	4.8812	-2.732	-1.602	5.7734	1.2642	2.6418	-0.0506	-0.1176	0.2556	0.1717	0.0479	0.5437	-0.3858	-0.5943	0.0041	0.1881	0.0471	0.0038	0.2594	-0.0622	0.2793	-32.9958	0.7959	41.3063
6	4.9042	4.4575	1.7451	4.539	1.6545	0.6267	-0.1402	0.212	-0.3424	-0.0348	0.1811	-0.1607	0.0028	0.1746	-0.0245	0.1873	-0.0061	0.0139	0.1655	-0.0176	0.2101	-2.4206	-10.7557	34.9734
7	1.612	0.6686	-0.0032	1.9242	0.0617	1.186	0.0122	0.1538	-0.0136	-0.0553	-0.0185	0.1796	0.0435	-0.1754	0.0093	0.1417	0.0021	-0.0196	0.1616	-0.019	0.1562	-24.7822	-8.7668	26.6454
8	4.4415	-1.7109	1.9112	2.0001	-0.7727	2.666	-0.0886	-0.1162	-0.0256	0.0119	0.0303	0.3005	-0.0865	-0.4798	0.0459	0.1181	-0.0028	-0.0121	0.1757	-0.0422	0.1977	-29.9347	-6.1009	32.3616
9	1.5324	0.419	0.8056	0.5005	0.603	1.5561	0.0229	-0.005	0.1728	-0.0064	-0.0626	0.0403	-0.0022	-0.0556	0.0481	0.1293	-0.0221	0.0009	0.1068	0.0088	0.1764	31.8151	7.2262	9.1627
10	1.2513	0.0781	0.1084	0.4314	0.3552	1.4106	0.0517	-0.1321	-0.1527	0.1106	-0.0645	0.0328	0.369	-0.143	0.0129	0.2294	-0.0679	-0.0076	0.1519	0.0095	0.192	31.4013	-4.9442	20.5088
11	1.18	0.3021	0.4329	0.6657	0.1995	0.4261	0.0297	-0.1469	0.0125	0.1528	-0.0114	-0.0156	0.0321	-0.0267	-0.0174	0.221	0.0036	-0.0031	0.1231	-0.0077	0.1506	-0.4754	-5.4923	57.7641
12	3.3623	2.0427	-0.4238	2.1705	-0.219	0.6566	-0.0143	-0.0748	0.1818	0.148	0.022	0.0846	-0.0204	-0.031	-0.0053	0.1858	0.0178	0.0071	0.109	-0.0209	0.1457	-1.4379	-0.6765	58.4696
13	3.4285	0.2271	-0.406	2.2826	-0.6501	3.5183	0.0884	-0.3967	-0.3194	0.4515	-0.0122	0.6386	0.1531	-0.5878	-0.081	0.2386	-0.0635	0.0599	0.3565	-0.0393	0.2669	-24.0262	-6.985	65.2907
14	1.257	-0.2281	-0.1738	0.3809	-0.0282	0.7979	0.0881	-0.1533	0.3512	0.0244	-0.0716	0.0688	-0.4282	0.0579	-0.0242	0.3073	-0.0398	-0.0133	0.1632	-0.0462	0.2811	-0.0682	12.7407	54.9484
15	2.8088	0.0145	-0.1977	1.4938	-0.3165	2.134	0.1053	-0.5035	0.3085	0.3683	-0.1296	0.1188	-0.1269	-0.0691	0.0204	0.3126	-0.0471	0.0223	0.281	-0.0903	0.1888	-8.317	2.1709	73.2154
16	0.7639	0.3415	-0.3843	1.9377	-1.9857	4.0866	0.0739	-0.5051	0.1703	0.2779	-0.0824	0.2569	-0.0684	-0.2462	0.0134	0.3162	-0.0267	0.0867	0.3636	-0.0807	0.1848	-18.032	1.1101	71.2677
17	1.5017	0.2303	0.0641	0.6796	0.7242	1.0293	0.0056	0.3567	-0.2491	-0.0459	0.189	-0.1971	0.2937	0.4925	-0.0015	0.196	0.0743	0.0235	0.3812	-0.1127	0.2812	58.1583	-4.9077	2.6435
18	2.915	0.3769	-0.6746	3.1331	-3.4234	9.4261	0.0256	0.2375	-0.0805	0.0348	0.2277	-0.1326	-0.0669	0.35	-0.2651	0.1441	0.0318	0.0295	0.2456	-0.1204	0.2633	56.4095	-1.3039	4.3747
19	2.7745	0.2177	-0.4486	1.554	1.0375	1.6328	-0.0285	0.0709	-0.2081	0.1021	0.1214	-0.1994	0.192	0.5324	-0.0784	0.1531	0.0754	-0.0152	0.3226	-0.0792	0.2554	62.7518	-0.3685	13.5313
20	3.1273	1.9084	2.6349	1.1907	1.6074	2.2208	-0.3225	0.6207	0.1747	-0.4098	0.3819	-0.0871	-0.5751	0.5494	-0.0755	0.266	-0.0851	0.033	0.3549	0.0096	0.2757	53.6025	13.0536	1.1704
21	4.3354	-0.7797	1.5237	4.0944	-0.4938	2.5854	-0.0864	-0.0268	0.2784	0.5912	0.3008	-0.1147	-0.2505	0.5318	-0.201	0.2402	-0.0162	0.0513	0.4087	-0.1282	0.3365	71.1678	11.5556	19.5063
22	1.7718	-0.2241	-0.0677	0.9313	0.7186	1.4308	-0.0042	0.1499	-0.013	0.0609	0.2605	-0.2902	0.0091	0.6513	-0.2058	0.2172	0.0556	0.0363	0.5576	-0.1448	0.3654	73.7931	2.057	10.7894
23	5.087	-2.4788	0.6661	2.855	-0.5942	0.345	-0.0827	-0.2783	-0.1378	0.1508	0.2251	-0.3468	0.1433	0.5037	-0.0609	0.1943	0.1059	-0.039	0.4686	-0.0981	0.2974	70.4809	1.5981	20.9567

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 9 through 132 )	A	9 - 132
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 133 through 174 )	A	133 - 174
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 175 through 199 )	A	175 - 199
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 200 through 219 )	A	200 - 219
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 220 through 240 )	A	220 - 240
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 241 through 264 )	A	241 - 264
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 265 through 349 )	A	265 - 349
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 350 through 383 )	A	350 - 383
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 9 through 155 )	B	9 - 155
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 156 through 383 )	B	156 - 383
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 9 through 174 )	C	9 - 174
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 175 through 219 )	C	175 - 219
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 220 through 240 )	C	220 - 240
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 241 through 268 )	C	241 - 268
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 269 through 349 )	C	269 - 349
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 350 through 383 )	C	350 - 383
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 9 through 174 )	D	9 - 174
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 175 through 199 )	D	175 - 199
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 200 through 240 )	D	200 - 240
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 241 through 264 )	D	241 - 264
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 265 through 300 )	D	265 - 300
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 301 through 349 )	D	301 - 349
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 350 through 383 )	D	350 - 383

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+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

-
Phasing

-
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