PDB-7w6g: TKS-L190G mutant from Cannabis sativa in complex with lauroyl-CoA

ID or keywords:

Entry

Database: PDB / ID: 7w6g

Title

TKS-L190G mutant from Cannabis sativa in complex with lauroyl-CoA

Components

3,5,7-trioxododecanoyl-CoA synthase

Keywords

LIGASE / tetraketide synthase / type III polypeptide synthase

Function / homology

Function and homology information

3,5,7-trioxododecanoyl-CoA synthase / Lyases; Carbon-sulfur lyases / cannabinoid biosynthetic process / polyketide biosynthetic process / terpenoid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / lyase activity
Similarity search - Function

Biological species

Cannabis sativa (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Nakashima, Y. / Lee, Y.E. / Morita, H.

Funding support

Japan, 1items

Citation

Journal: Org.Lett. / Year: 2022
Title: Dual Engineering of Olivetolic Acid Cyclase and Tetraketide Synthase to Generate Longer Alkyl-Chain Olivetolic Acid Analogs.
Authors: Lee, Y.E. / Nakashima, Y. / Kodama, T. / Chen, X. / Morita, H.

History

Deposition	Dec 1, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7w6g.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb7w6g.ent.gz	743.3 KB	Display	PDB format
PDBx/mmJSON format	7w6g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7w6g_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	7w6g_full_validation.pdf.gz	1.4 MB	Display
Data in XML	7w6g_validation.xml.gz	62.2 KB	Display
Data in CIF	7w6g_validation.cif.gz	85.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/7w6g ftp://data.pdbj.org/pub/pdb/validation_reports/w6/7w6g	HTTPS FTP

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Related structure data

Related structure data	7w6dC 7w6eC 7w6fC 6gw3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5wc4-d 4ydr-d 6gw3-1 7w6g-2 3ov2-1 7vf0-2 3ov3-1 1mqq-d 3ov3-2 1ee0-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	#90 - Jun 2007 Fatty Acid Synthase similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: 3,5,7-trioxododecanoyl-CoA synthase

B: 3,5,7-trioxododecanoyl-CoA synthase

C: 3,5,7-trioxododecanoyl-CoA synthase

D: 3,5,7-trioxododecanoyl-CoA synthase

hetero molecules

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

1

A: 3,5,7-trioxododecanoyl-CoA synthase

C: 3,5,7-trioxododecanoyl-CoA synthase

hetero molecules

defined by author&software
Evidence: gel filtration
87.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 3,5,7-trioxododecanoyl-CoA synthase

D: 3,5,7-trioxododecanoyl-CoA synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.021, 66.930, 95.094
Angle α, β, γ (deg.)	93.449, 102.107, 100.196
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	3,5,7-trioxododecanoyl-CoA synthase / Olivetol synthase / Polyketide synthase-1 / Tetraketide synthase Mass: 42617.969 Da / Num. of mol.: 4 / Mutation: L190G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cannabis sativa (plant) / Gene: OLS, CAN24, PKS-1, TKS / Production host: Escherichia coli (E. coli) References: UniProt: B1Q2B6, 3,5,7-trioxododecanoyl-CoA synthase, Lyases; Carbon-sulfur lyases

#1: Protein

3,5,7-trioxododecanoyl-CoA synthase / Olivetol synthase / Polyketide synthase-1 / Tetraketide synthase

Mass: 42617.969 Da / Num. of mol.: 4 / Mutation: L190G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Cannabis sativa (plant) / Gene: OLS, CAN24, PKS-1, TKS / Production host:

Escherichia coli (E. coli)
References: UniProt: B1Q2B6, 3,5,7-trioxododecanoyl-CoA synthase, Lyases; Carbon-sulfur lyases

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Non-polymers , 6 types, 638 molecules

#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-8I9 / ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] tridecanethioate Mass: 963.863 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₆₀N₇O₁₇P₃S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	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: 2.07 Å³/Da / Density % sol: 40.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium acetate, 20% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.07 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 31, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07 Å / Relative weight: 1
Reflection	Resolution: 2.1→47.18 Å / Num. obs: 148561 / % possible obs: 97.6 % / Redundancy: 3.5 % / B_iso Wilson estimate: 23.29 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.112 / R_rim(I) all: 0.155 / Net I/σ(I): 4.8
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.807 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4413 / CC_1/2: 0.684 / R_rim(I) all: 1.117 / % possible all: 96.4

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
pointless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6GW3

6gw3

Resolution: 2.1→47.18 Å / SU ML: 0.2657 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 26.5107
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2359	7306	4.92 %
R_work	0.1935	141255	-
obs	0.1957	148561	92.91 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.9 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→47.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11738	0	156	621	12515

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0036	12484
X-RAY DIFFRACTION	f_angle_d	0.6172	16898
X-RAY DIFFRACTION	f_chiral_restr	0.0432	1883
X-RAY DIFFRACTION	f_plane_restr	0.0035	2175
X-RAY DIFFRACTION	f_dihedral_angle_d	19.3368	4646

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 (%)
2.1-2.12	0.355	201	0.3216	4780	X-RAY DIFFRACTION	93.63
2.12-2.15	0.3277	239	0.3054	4772	X-RAY DIFFRACTION	93.38
2.15-2.18	0.3177	243	0.2887	4717	X-RAY DIFFRACTION	93.76
2.18-2.2	0.3	248	0.279	4716	X-RAY DIFFRACTION	93.55
2.2-2.23	0.3451	307	0.2804	4856	X-RAY DIFFRACTION	93.57
2.23-2.26	0.2966	241	0.2686	4538	X-RAY DIFFRACTION	92.87
2.26-2.29	0.3265	281	0.2582	4764	X-RAY DIFFRACTION	93.63
2.29-2.33	0.2977	243	0.2607	4717	X-RAY DIFFRACTION	93.44
2.33-2.37	0.2812	247	0.2472	4705	X-RAY DIFFRACTION	93.68
2.37-2.4	0.3212	254	0.2398	4796	X-RAY DIFFRACTION	93.52
2.4-2.45	0.2421	257	0.2394	4668	X-RAY DIFFRACTION	93.07
2.45-2.49	0.2824	284	0.2271	4696	X-RAY DIFFRACTION	93.54
2.49-2.54	0.2841	246	0.2251	4695	X-RAY DIFFRACTION	92.7
2.54-2.59	0.2824	230	0.2119	4754	X-RAY DIFFRACTION	93.26
2.59-2.65	0.2597	213	0.2118	4753	X-RAY DIFFRACTION	93.1
2.65-2.71	0.2849	236	0.2076	4683	X-RAY DIFFRACTION	92.67
2.71-2.77	0.2827	233	0.2136	4717	X-RAY DIFFRACTION	92.08
2.78-2.85	0.2435	264	0.203	4550	X-RAY DIFFRACTION	91.73
2.85-2.93	0.2408	203	0.1939	4648	X-RAY DIFFRACTION	90.17
2.93-3.03	0.2431	262	0.1824	4579	X-RAY DIFFRACTION	90.38
3.03-3.14	0.2212	244	0.1788	4569	X-RAY DIFFRACTION	91.64
3.14-3.26	0.196	187	0.1672	4760	X-RAY DIFFRACTION	92.12
3.26-3.41	0.1927	249	0.1582	4823	X-RAY DIFFRACTION	94.73
3.41-3.59	0.1945	229	0.1464	4791	X-RAY DIFFRACTION	94.4
3.59-3.82	0.1794	229	0.1405	4827	X-RAY DIFFRACTION	94.4
3.82-4.11	0.1893	217	0.1433	4735	X-RAY DIFFRACTION	93.33
4.11-4.52	0.1869	274	0.1353	4679	X-RAY DIFFRACTION	92.51
4.52-5.18	0.1704	246	0.1415	4744	X-RAY DIFFRACTION	93.48
5.18-6.52	0.2314	223	0.1903	4730	X-RAY DIFFRACTION	93.7
6.52-47.18	0.1963	276	0.1867	4493	X-RAY DIFFRACTION	89.24

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	1.31168455233	0.131484680369	-0.0121457977249	0.672866803988	0.470056296709	1.36363153684	0.14105112288	-0.142244151157	-0.240888597567	0.281673142559	-0.131180066742	0.07263184091	0.421007520825	-0.138094185161	-0.0484189600656	0.420118438522	-0.0489188843492	-0.0075141763129	0.247088620256	0.0153566140289	0.237742702624	10.28194319	25.5087859326	28.9290663709
2	0.707677511825	0.291927718349	0.188040626642	1.35027254372	0.725568286732	1.14552952541	0.0203865508786	0.11920908365	-0.205392472471	0.0205873383918	0.0712715098769	-0.0629487388868	0.215977864121	0.125858829229	-0.0488566496468	0.192195916321	0.0225707626468	-0.0173172003659	0.172310219539	0.00618777339178	0.153524898839	21.5733890357	31.7108060628	15.8293184388
3	1.12749974725	-0.340227072515	-0.186132075507	0.50105266417	0.457669016834	0.855316228995	-0.00167325142769	-0.129610446788	-0.27255885207	0.455951033857	-0.0588693564577	0.102201715741	0.516715733189	-0.325398293637	0.0716496054142	0.566086996599	-0.162520513955	0.0414638613484	0.38569074163	0.0240214482148	0.342674481974	29.096024573	20.3846916759	72.8407778726
4	0.411748600914	0.104034083245	0.0169248837891	1.34911442136	0.555867702621	1.05371352356	0.037188803818	-0.0507708143373	-0.079465665163	0.276425750547	-0.058681988984	-0.0609263930773	0.293031541825	-0.123839818843	0.0232211745945	0.246674078737	-0.0164983529337	-0.0243103869232	0.159525575989	0.0107222373305	0.17798195755	40.8314225544	27.7220117121	60.5671320587
5	0.474952781819	0.498581991753	0.372902910545	0.882350305357	0.542138767672	0.713694338918	-0.0397678424019	-0.144915623568	0.218630567121	-0.0274489051082	-0.239740529823	0.367422560136	-0.175787801412	-0.183983642989	0.152313596272	0.215919711662	-0.0133354996593	0.0147607703086	0.308187708214	-0.100688709708	0.332582107423	14.2619937931	66.2595719894	35.0311797053
6	0.561445798206	0.233966404281	0.177465544036	1.05991680316	0.394774061607	1.30980565705	-0.100989349519	0.0990911038313	0.101877000536	-0.225420263123	0.0617185594986	0.219176738866	-0.187649009305	0.0585423569391	0.0252703227401	0.222448432997	-0.0094122342483	-0.0590001982006	0.170067244044	0.0135480733925	0.135832220817	18.9646431583	53.4028488144	15.5662344689
7	1.29068465321	0.0957754545135	-0.154728655442	1.40922090255	0.966064289069	1.45026643242	0.0552599878305	-0.10449562111	0.116526361553	0.0767399495532	-0.107922419601	0.259349940166	-0.151628816089	0.0202387697139	0.00327857424639	0.142517074817	-0.0563201627262	0.033158262828	0.255728154697	-0.0455569323434	0.214843733983	19.3858151968	58.4663314686	30.3946286279
8	0.766602279286	0.207755159529	0.436247975065	0.813010175164	0.478482355224	0.420912815875	-0.0701000871399	0.0596140067914	0.0258094707811	-0.0646571406106	0.0890599954509	-0.100269254083	0.00304080298517	0.20525099923	-0.0622712596309	0.163908931023	-0.0406390099031	0.0300336475892	0.318158196118	-0.0290709446584	0.162021864142	30.2922482092	56.5707569465	26.1012209289
9	1.84665853716	0.0674029562503	-0.545520408015	0.361145643852	-0.366154853684	0.496720026594	-0.0301859869131	-0.00868693562956	0.149956139292	-0.0554833374492	0.17747611545	-0.24028946964	-0.100016679126	0.389630667025	-0.0898176468924	0.15258020403	-0.0942762156259	0.0200791966499	0.419116780728	-0.0748138598696	0.272347635426	42.6689229555	64.7598159329	28.4173990646
10	1.24066497953	0.370390333457	-0.505768184249	1.04210477233	-0.00203211238494	1.04125072356	0.0481879427996	0.106437955684	0.164501854556	-0.141523957565	0.0714778965649	-0.0395336478377	-0.36220854778	0.29785714508	-0.111483257244	0.296929409596	-0.109153102152	0.0051901777926	0.31635961276	-0.0282842150371	0.188757203188	33.71717075	67.1504157025	20.0795559691
11	0.799884321613	0.00411119064568	0.112809456421	1.11351279611	0.227292876274	1.01196925595	-0.0208824679913	-0.232801262147	0.0702163323516	0.377875400405	-0.213799046689	0.0907764900162	-0.0858897414289	-0.362389396954	0.130844475833	0.233413585809	-0.00336588387617	0.0135601667661	0.256730528973	-0.0407715292237	0.19466819212	33.3815727396	58.4226269695	77.6328999879
12	0.7578005867	0.0192075221447	0.0590208798765	1.27762644393	0.397513907123	1.03727413059	-0.00427621633565	-0.0999828933451	0.131809947562	0.262890567062	-0.0203506973763	-0.211454874072	0.0391032497401	-0.0154465564552	0.0144337145714	0.193735003695	0.0145380244459	-0.0473091063295	0.130620604722	-0.00352851555826	0.186071515742	48.7472240473	54.7684411601	69.2536428266

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 83 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 84 through 385 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 3 through 83 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 84 through 383 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 4 through 83 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 84 through 173 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 174 through 207 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 208 through 272 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 273 through 318 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 319 through 385 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 3 through 110 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 111 through 385 )

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 6 types, 638 molecules

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