PDB-7w6e: Polyketide cyclase OAC-F24I mutant from Cannabis sativa in comple...

ID or keywords:

Entry

Database: PDB / ID: 7w6e

Title

Polyketide cyclase OAC-F24I mutant from Cannabis sativa in complex with 6-heptylresorcylic acid

Components

Olivetolic acid cyclase

Keywords

LYASE / olivetolic acid cyclase / polypeptide cyclase

Function / homology

Function and homology information

olivetolic acid cyclase / olivetolic acid biosynthetic process / cannabinoid biosynthetic process / pollen tube adhesion / cyclase activity / terpenoid biosynthetic process / lyase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Cannabis sativa (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.38 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7w6e.cif.gz	190.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7w6e.ent.gz	126.2 KB	Display	PDB format
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Validation report

Summary document	7w6e_validation.pdf.gz	907.3 KB	Display	wwPDB validaton report
Full document	7w6e_full_validation.pdf.gz	908.6 KB	Display
Data in XML	7w6e_validation.xml.gz	14.5 KB	Display
Data in CIF	7w6e_validation.cif.gz	21.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/7w6e ftp://data.pdbj.org/pub/pdb/validation_reports/w6/7w6e	HTTPS FTP

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Related structure data

Related structure data	7w6dC 7w6fC 7w6gC 5b08S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7w6f-d 2cbq-3 4l1h-2 6uup-3 1a7r-d 1ohq-d 4wkw-1 6b89-2 3cdy-d 6uup-1 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

Deposited unit

A: Olivetolic acid cyclase

B: Olivetolic acid cyclase

hetero molecules

24.9 kDa, 2 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)	32.574, 39.453, 43.083
Angle α, β, γ (deg.)	71.144, 76.495, 67.510
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	Olivetolic acid cyclase Mass: 12195.995 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cannabis sativa (plant) / Gene: OAC / Production host: Escherichia coli M15 (bacteria) / References: UniProt: I6WU39, olivetolic acid cyclase
#2: Chemical	ChemComp-8HL / 2-heptyl-4,6-bis(oxidanyl)benzoic acid Mass: 252.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 324 / 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: 1.97 Å³/Da / Density % sol: 37.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 35% 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: Dec 19, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07 Å / Relative weight: 1
Reflection	Resolution: 1.38→40.45 Å / Num. obs: 70848 / % possible obs: 94.8 % / Redundancy: 4.1 % / B_iso Wilson estimate: 12.23 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.042 / R_rim(I) all: 0.057 / Net I/σ(I): 14.3
Reflection shell	Resolution: 1.38→1.4 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.263 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1781 / CC_1/2: 0.936 / R_rim(I) all: 0.353 / % possible all: 92.5

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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: 5B08

5b08

Resolution: 1.38→40.45 Å / SU ML: 0.1186 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 16.4323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.162	3555	5.02 %
R_work	0.1362	67293	-
obs	0.1375	70848	92.47 %

Solvent computation

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

Displacement parameters

B_iso mean: 17.34 Å²

Refinement step

Cycle: LAST / Resolution: 1.38→40.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1759	0	0	324	2083

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0111	2043
X-RAY DIFFRACTION	f_angle_d	1.2254	2802
X-RAY DIFFRACTION	f_chiral_restr	0.0973	300
X-RAY DIFFRACTION	f_plane_restr	0.0081	361
X-RAY DIFFRACTION	f_dihedral_angle_d	21.4444	768

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 (%)
1.38-1.4	0.2269	149	0.2175	2644	X-RAY DIFFRACTION	88.67
1.4-1.42	0.259	129	0.2123	2661	X-RAY DIFFRACTION	90.58
1.42-1.44	0.2204	127	0.2009	2624	X-RAY DIFFRACTION	91.21
1.44-1.46	0.1991	143	0.1953	2663	X-RAY DIFFRACTION	91.46
1.46-1.49	0.2376	176	0.1796	2727	X-RAY DIFFRACTION	93.16
1.49-1.51	0.1783	112	0.1851	2638	X-RAY DIFFRACTION	92.22
1.51-1.54	0.196	140	0.1832	2723	X-RAY DIFFRACTION	92.65
1.54-1.57	0.2389	143	0.1733	2691	X-RAY DIFFRACTION	92.98
1.57-1.6	0.1794	172	0.1641	2687	X-RAY DIFFRACTION	93.19
1.6-1.64	0.1502	143	0.1607	2753	X-RAY DIFFRACTION	93.36
1.64-1.67	0.1922	144	0.1535	2679	X-RAY DIFFRACTION	93.41
1.67-1.72	0.1747	143	0.1501	2764	X-RAY DIFFRACTION	93.83
1.72-1.76	0.1796	154	0.1566	2685	X-RAY DIFFRACTION	93.51
1.76-1.81	0.1906	160	0.1567	2726	X-RAY DIFFRACTION	95
1.81-1.87	0.1935	128	0.1499	2775	X-RAY DIFFRACTION	93.71
1.87-1.94	0.179	140	0.1419	2710	X-RAY DIFFRACTION	94.06
1.94-2.02	0.1482	138	0.1332	2760	X-RAY DIFFRACTION	94.09
2.02-2.11	0.1441	152	0.1287	2659	X-RAY DIFFRACTION	93.08
2.11-2.22	0.1486	164	0.1325	2710	X-RAY DIFFRACTION	93.07
2.22-2.36	0.1272	126	0.1203	2762	X-RAY DIFFRACTION	93.71
2.36-2.54	0.1441	130	0.1163	2693	X-RAY DIFFRACTION	92.62
2.54-2.8	0.1388	175	0.1202	2628	X-RAY DIFFRACTION	92.02
2.8-3.2	0.136	122	0.1201	2670	X-RAY DIFFRACTION	90.65
3.2-4.03	0.1332	125	0.1062	2654	X-RAY DIFFRACTION	89.99
4.03-40.45	0.1805	120	0.1263	2607	X-RAY DIFFRACTION	89.7

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	0.152256003357	0.135364544592	0.0984457789616	0.0843680656454	0.0594738824621	0.0286733221457	0.0788171391663	0.0503822867554	0.0321436222853	-0.0173102640162	-0.023851410944	-0.0694737210137	-0.0376100693919	0.015765750309	0.0222363941309	0.0727143976766	0.000733937450035	0.0082918426617	0.0880768918458	0.00643478819136	0.101485913906	17.4687198374	10.3779350608	9.84858589711
2	0.187715061913	0.263293569729	-0.0481164729851	0.458030122382	0.150739599232	0.677688076636	-0.0736465332357	-0.056301181599	0.14841363067	0.156612308448	0.0321835930819	-0.10191495133	0.0414366544394	0.0217089989066	-0.0125694030607	0.0813825348466	0.00680879084554	-0.0118961399628	0.0679812001117	0.00699493365251	0.0698584393051	12.2261362635	10.6034096422	22.3945380049
3	0.217528612563	0.187580523873	-0.0916108769435	0.244442214501	0.157320222077	0.356052513373	0.041445057677	0.0732812645198	-0.0477952714907	0.0765078095468	0.021078588138	0.099277903952	-0.0886663624173	-0.0445630603667	0.017122613662	0.0925354973676	0.0146523840615	-0.00460236458578	0.109981936373	0.00121889556171	0.13483925916	10.5329230105	21.7363813703	10.18328694
4	0.387633582879	-0.34753568684	-0.188176396692	0.728710950424	-0.0728588609287	0.393920143724	-0.00339520190861	0.00589941727709	0.00367236966572	-0.017793317647	-0.0416183187105	-0.0203066806504	0.0701890399163	0.0220263983157	-0.0138307260722	0.0741957648457	0.00271916688505	-0.0062668386648	0.0819887868065	-0.000147522907299	0.0866004659874	13.8381121559	5.98579724785	12.18232043
5	0.219557317659	-0.111143049921	-0.37290375861	0.456691460692	0.117369345162	0.453888700208	0.0257706379523	0.011687067992	-0.0428555741582	-0.00192207473142	0.027558587405	-0.100895738123	0.0437478941977	-0.00251092373048	0.000284826056442	0.0920875634605	-0.000518690700243	-0.00223571450693	0.0853714791945	-0.0002862991204	0.0967822086684	19.7597596604	19.3677204212	-5.31041895009
6	0.0117159425401	-0.0273094463276	-0.25543996103	0.474945905542	-0.290170834747	0.443746164026	-0.031779080148	-0.00264990828203	-0.0455142498093	-0.0225554963876	0.00959693376657	-0.0972971561527	-0.0138582588883	-0.026456655365	3.60748190774E-5	0.0956754269056	-0.00323080444535	-0.00737959508408	0.0871398946549	-0.000713492195593	0.116176548989	17.0852018203	14.0041833738	-0.0855174125455
7	0.366679231341	0.0570085719414	0.0329506191343	0.232235118145	-0.0250586902458	0.0352161499572	0.00165771994418	-0.00158267085834	0.00228972528533	-0.01042107321	0.0069831754195	-0.0271625512124	-0.071067642695	0.031677925107	4.71981831081E-5	0.0770732605749	-0.0164799143245	0.00393884290151	0.0510700062126	0.00450053950715	0.0447949671277	19.1992973284	28.4567349101	-2.21492277725
8	0.22966724981	0.3391767817	-0.0499075347122	0.378240744208	0.0462174219885	0.106930829202	0.0526891213669	0.000244280506679	-0.0986696217756	0.0236450258633	-0.0250603984633	-0.0108427383525	0.0992278831719	0.0316428701445	-0.00328597268087	0.0838009368411	0.00549638371804	-0.00209355986084	0.120816168276	-0.00576775769135	0.0964581529934	13.7636928704	20.5422853935	2.91888796225

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 56 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 57 through 101 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -2 through 32 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 33 through 56 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 57 through 85 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 86 through 101 )

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