PDB-6rt8: Structure of catharanthine synthase - an alpha-beta hydrolase fro...

ID or keywords:

Entry

Database: PDB / ID: 6rt8

Title

Structure of catharanthine synthase - an alpha-beta hydrolase from Catharanthus roseus with a cleaviminium intermediate bound

Components

Catharanthine synthase

Keywords

HYDROLASE / alkaloid / catharanthine / natural product / biosynthesis / alpha/beta hydrolase fold

Function / homology

Function and homology information

Lyases / alkaloid metabolic process / hydrolase activity / lyase activity / nucleus / cytosol
Similarity search - Function

Biological species

Catharanthus roseus (Madagascar periwinkle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.19 Å

Authors

Caputi, L. / Franke, J. / Bussey, K. / Farrow, S.C. / Curcino Vieira, I.J. / Stevenson, C.E.M. / Lawson, D.M. / O'Connor, S.E.

Funding support

Belgium,

United Kingdom, 2items

Citation

Journal: Nat.Chem.Biol. / Year: 2020
Title: Structural basis of cycloaddition in biosynthesis of iboga and aspidosperma alkaloids.
Authors: Caputi, L. / Franke, J. / Bussey, K. / Farrow, S.C. / Vieira, I.J.C. / Stevenson, C.E.M. / Lawson, D.M. / O'Connor, S.E.

History

Deposition	May 22, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 4, 2020	Provider: repository / Type: Initial release
Revision 1.1	Apr 1, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 24, 2024	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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6rt8.cif.gz	998.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6rt8.ent.gz	831.6 KB	Display	PDB format
PDBx/mmJSON format	6rt8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6rt8_validation.pdf.gz	3.1 MB	Display	wwPDB validaton report
Full document	6rt8_full_validation.pdf.gz	3.2 MB	Display
Data in XML	6rt8_validation.xml.gz	90.5 KB	Display
Data in CIF	6rt8_validation.cif.gz	122.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rt/6rt8 ftp://data.pdbj.org/pub/pdb/validation_reports/rt/6rt8	HTTPS FTP

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Related structure data

Related structure data	6rj8C 6rs4SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6rs4-d 2fr4-1 3mwp-3 1k3u-d 1kie-d 1tcc-d 4hdn-d 3mx5-2 4s0x-d 4i73-1 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) 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

6rj8C

6rs4SC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Catharanthine synthase

B: Catharanthine synthase

C: Catharanthine synthase

D: Catharanthine synthase

E: Catharanthine synthase

F: Catharanthine synthase

G: Catharanthine synthase

H: Catharanthine synthase

hetero molecules

300 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Catharanthine synthase

B: Catharanthine synthase

hetero molecules

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

2

C: Catharanthine synthase

D: Catharanthine synthase

hetero molecules

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

3

E: Catharanthine synthase

F: Catharanthine synthase

hetero molecules

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

4

G: Catharanthine synthase

H: Catharanthine synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.540, 121.030, 157.980
Angle α, β, γ (deg.)	90.000, 99.020, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	LYS	LYS	A	A	9 - 327	10 - 328
2	1	ASP	ASP	LYS	LYS	B	B	9 - 327	10 - 328
1	2	ASP	ASP	LYS	LYS	A	A	9 - 327	10 - 328
2	2	ASP	ASP	LYS	LYS	C	C	9 - 327	10 - 328
1	3	ASP	ASP	LYS	LYS	A	A	9 - 327	10 - 328
2	3	ASP	ASP	LYS	LYS	D	D	9 - 327	10 - 328
1	4	ASP	ASP	ILE	ILE	A	A	9 - 326	10 - 327
2	4	ASP	ASP	ILE	ILE	E	E	9 - 326	10 - 327
1	5	ASP	ASP	LYS	LYS	A	A	9 - 327	10 - 328
2	5	ASP	ASP	LYS	LYS	F	F	9 - 327	10 - 328
1	6	ASP	ASP	LYS	LYS	A	A	9 - 327	10 - 328
2	6	ASP	ASP	LYS	LYS	G	G	9 - 327	10 - 328
1	7	GLU	GLU	ILE	ILE	A	A	10 - 326	11 - 327
2	7	GLU	GLU	ILE	ILE	H	H	10 - 326	11 - 327
1	8	ASP	ASP	LYS	LYS	B	B	9 - 327	10 - 328
2	8	ASP	ASP	LYS	LYS	C	C	9 - 327	10 - 328
1	9	ASP	ASP	LYS	LYS	B	B	9 - 327	10 - 328
2	9	ASP	ASP	LYS	LYS	D	D	9 - 327	10 - 328
1	10	ASP	ASP	ILE	ILE	B	B	9 - 326	10 - 327
2	10	ASP	ASP	ILE	ILE	E	E	9 - 326	10 - 327
1	11	ASP	ASP	LYS	LYS	B	B	9 - 327	10 - 328
2	11	ASP	ASP	LYS	LYS	F	F	9 - 327	10 - 328
1	12	ASP	ASP	LYS	LYS	B	B	9 - 327	10 - 328
2	12	ASP	ASP	LYS	LYS	G	G	9 - 327	10 - 328
1	13	GLU	GLU	ILE	ILE	B	B	10 - 326	11 - 327
2	13	GLU	GLU	ILE	ILE	H	H	10 - 326	11 - 327
1	14	ASP	ASP	LYS	LYS	C	C	9 - 327	10 - 328
2	14	ASP	ASP	LYS	LYS	D	D	9 - 327	10 - 328
1	15	ASP	ASP	ILE	ILE	C	C	9 - 326	10 - 327
2	15	ASP	ASP	ILE	ILE	E	E	9 - 326	10 - 327
1	16	ASP	ASP	LYS	LYS	C	C	9 - 327	10 - 328
2	16	ASP	ASP	LYS	LYS	F	F	9 - 327	10 - 328
1	17	ASP	ASP	LYS	LYS	C	C	9 - 327	10 - 328
2	17	ASP	ASP	LYS	LYS	G	G	9 - 327	10 - 328
1	18	GLU	GLU	ILE	ILE	C	C	10 - 326	11 - 327
2	18	GLU	GLU	ILE	ILE	H	H	10 - 326	11 - 327
1	19	ASP	ASP	ILE	ILE	D	D	9 - 326	10 - 327
2	19	ASP	ASP	ILE	ILE	E	E	9 - 326	10 - 327
1	20	ASP	ASP	LYS	LYS	D	D	9 - 327	10 - 328
2	20	ASP	ASP	LYS	LYS	F	F	9 - 327	10 - 328
1	21	ASP	ASP	LYS	LYS	D	D	9 - 327	10 - 328
2	21	ASP	ASP	LYS	LYS	G	G	9 - 327	10 - 328
1	22	GLU	GLU	ILE	ILE	D	D	10 - 326	11 - 327
2	22	GLU	GLU	ILE	ILE	H	H	10 - 326	11 - 327
1	23	ASP	ASP	ILE	ILE	E	E	9 - 326	10 - 327
2	23	ASP	ASP	ILE	ILE	F	F	9 - 326	10 - 327
1	24	ASP	ASP	ILE	ILE	E	E	9 - 326	10 - 327
2	24	ASP	ASP	ILE	ILE	G	G	9 - 326	10 - 327
1	25	GLU	GLU	ILE	ILE	E	E	10 - 326	11 - 327
2	25	GLU	GLU	ILE	ILE	H	H	10 - 326	11 - 327
1	26	ASP	ASP	LYS	LYS	F	F	9 - 327	10 - 328
2	26	ASP	ASP	LYS	LYS	G	G	9 - 327	10 - 328
1	27	GLU	GLU	ILE	ILE	F	F	10 - 326	11 - 327
2	27	GLU	GLU	ILE	ILE	H	H	10 - 326	11 - 327
1	28	GLU	GLU	ILE	ILE	G	G	10 - 326	11 - 327
2	28	GLU	GLU	ILE	ILE	H	H	10 - 326	11 - 327

NCS ensembles :

#1: Protein	Catharanthine synthase / Hydrolase 1 / CrHL1 Mass: 37076.957 Da / Num. of mol.: 8 Mutation: Native N-terminal MET is replaced by a GLY-PRO dipeptide left over from cleavage of the affinity tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle) Gene: CS, HL1, Caros025416 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SOLUBL21 / References: UniProt: A0A2P1GIW2, Lyases
#2: Chemical	ChemComp-KJE / 18-carboxymethoxy-cleaviminium Mass: 337.435 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₅N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.6 Å³/Da / Density % sol: 52.61 % / Description: NULL
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NULL

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.9763 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.9763 Å / Relative weight: 1

Reflection

Resolution: 2.19→52.01 Å / Num. obs: 152727 / % possible obs: 98.3 % / Redundancy: 7 % / B_iso Wilson estimate: 41.2 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.093 / R_pim(I) all: 0.038 / R_rim(I) all: 0.1 / Net I/σ(I): 14.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2.19-2.23	7	1.129	52594	7478	0.559	0.457	1.219	2	97.7
12-52.01	6.6	0.022	6260	945	0.999	0.009	0.024	71.1	95.8

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Processing

Software

Name	Version	Classification
XDS	20161101	data reduction
Aimless	0.7.4	data scaling
REFMAC	5.8.0238	refinement
PDB_EXTRACT	3.25	data extraction
PHASER	2.7.17	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6RS4

6rs4

Resolution: 2.19→52.01 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.952 / SU B: 21.651 / SU ML: 0.228 / SU R Cruickshank DPI: 0.2427 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.196
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2342	7594	5 %	RANDOM
R_work	0.1939	-	-	-
obs	0.1959	145106	98.1 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å

Displacement parameters

B_iso max: 202.59 Å² / B_iso mean: 62.531 Å² / B_iso min: 27.34 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.78 Å²	0 Å²	2.8 Å²
2-	-	0.88 Å²	0 Å²
3-	-	-	-0.94 Å²

Refinement step

Cycle: final / Resolution: 2.19→52.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19468	0	276	388	20132
B_iso mean	-	-	67.91	54.54	-
Num. residues	-	-	-	-	2501

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	20341
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	18236
X-RAY DIFFRACTION	r_angle_refined_deg	1.522	1.642	27773
X-RAY DIFFRACTION	r_angle_other_deg	1.269	1.575	42165
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.215	5	2483
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.655	22.582	945
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.221	15	2945
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.943	15	76
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	2653
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	22813
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4411

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	10407	0.05
1	2	B	10407	0.05
2	1	A	10493	0.04
2	2	C	10493	0.04
3	1	A	10479	0.04
3	2	D	10479	0.04
4	1	A	9755	0.06
4	2	E	9755	0.06
5	1	A	10357	0.04
5	2	F	10357	0.04
6	1	A	10503	0.04
6	2	G	10503	0.04
7	1	A	10235	0.05
7	2	H	10235	0.05
8	1	B	10422	0.06
8	2	C	10422	0.06
9	1	B	10426	0.05
9	2	D	10426	0.05
10	1	B	9815	0.04
10	2	E	9815	0.04
11	1	B	10265	0.05
11	2	F	10265	0.05
12	1	B	10434	0.04
12	2	G	10434	0.04
13	1	B	10234	0.05
13	2	H	10234	0.05
14	1	C	10468	0.05
14	2	D	10468	0.05
15	1	C	9758	0.06
15	2	E	9758	0.06
16	1	C	10359	0.05
16	2	F	10359	0.05
17	1	C	10499	0.05
17	2	G	10499	0.05
18	1	C	10255	0.05
18	2	H	10255	0.05
19	1	D	9744	0.06
19	2	E	9744	0.06
20	1	D	10349	0.04
20	2	F	10349	0.04
21	1	D	10512	0.03
21	2	G	10512	0.03
22	1	D	10294	0.04
22	2	H	10294	0.04
23	1	E	9732	0.05
23	2	F	9732	0.05
24	1	E	9761	0.05
24	2	G	9761	0.05
25	1	E	9632	0.05
25	2	H	9632	0.05
26	1	F	10388	0.04
26	2	G	10388	0.04
27	1	F	10102	0.04
27	2	H	10102	0.04
28	1	G	10271	0.04
28	2	H	10271	0.04

LS refinement shell

Resolution: 2.19→2.247 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.39	588	-
R_work	0.408	10578	-
all	-	11166	-
obs	-	-	97.46 %

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	1.6503	-0.3113	-0.0283	1.1178	-0.1171	2.3728	0.123	-0.0524	0.1205	0.077	0.0419	0.0185	-0.2314	-0.132	-0.1649	0.0962	0.0473	0.0958	0.1066	0.0308	0.1068	81.9742	-9.7566	18.9403
2	2.2994	0.3109	0.3325	1.4933	0.1416	2.6992	-0.0213	0.0566	-0.1098	-0.0396	0.202	0.1087	-0.0606	-0.3454	-0.1807	0.0404	0.086	0.059	0.2825	0.1639	0.1139	74.186	-13.0321	-18.0666
3	2.3368	0.5694	-0.6902	2.0218	-0.0691	2.088	-0.067	0.0238	-0.1711	-0.1511	0.0737	0.117	0.0605	-0.2026	-0.0067	0.0815	0.0167	0.0373	0.1701	0.03	0.0582	64.7312	-4.9775	104.1061
4	1.7496	0.2459	-0.6801	3.1653	-0.3432	1.8942	0.0502	-0.0356	0.1197	-0.1542	-0.0115	-0.0758	-0.1771	-0.0017	-0.0387	0.119	0.0008	0.0697	0.1571	-0.041	0.0619	88.9907	20.2914	88.8966
5	4.9709	0.2462	-0.7429	1.5954	0.3737	2.8568	-0.0426	-1.3348	-0.7515	0.1816	-0.1953	-0.1561	0.2047	0.0549	0.238	0.0394	0.011	0.0495	0.4692	0.3286	0.388	38.1073	11.7596	10.9934
6	4.0097	1.4138	-0.9154	2.13	-0.4955	1.7328	-0.3454	0.8395	-0.4088	-0.2296	0.2416	0.0376	0.0213	-0.2438	0.1038	0.0437	-0.0592	0.0351	0.2445	-0.124	0.1704	45.8892	21.543	-24.2025
7	2.107	-0.3883	-0.5911	1.8118	0.1906	1.9828	0.2214	0.0218	0.3384	-0.0197	-0.1286	0.0755	-0.3057	-0.0402	-0.0928	0.2428	0.0051	0.1783	0.1716	0.0068	0.1722	36.1917	21.951	64.3078
8	2.9767	-0.7752	-1.478	3.1705	-0.1004	2.728	0.1209	-0.3355	0.0995	0.1758	-0.017	-0.406	-0.1592	0.431	-0.104	0.1909	-0.0035	0.0632	0.24	-0.0074	0.0989	64.012	-0.3622	50.8484

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 401
2	X-RAY DIFFRACTION	2	B	9 - 401
3	X-RAY DIFFRACTION	3	C	9 - 401
4	X-RAY DIFFRACTION	4	D	9 - 401
5	X-RAY DIFFRACTION	5	E	9 - 401
6	X-RAY DIFFRACTION	6	F	9 - 401
7	X-RAY DIFFRACTION	7	G	9 - 401
8	X-RAY DIFFRACTION	8	H	9 - 401

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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

-
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

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Yorodumi