PDB-6vya: Crystal structure of NotF in complex with brevianamide F and DMSPP

ID or keywords:

Entry

Database: PDB / ID: 6vya

Title

Crystal structure of NotF in complex with brevianamide F and DMSPP

Components

Deoxybrevianamide E synthase notF

Keywords

TRANSFERASE / Fungal indole prenyltransferase

Function / homology

Function and homology information

brevianamide F prenyltransferase (deoxybrevianamide E-forming) / alkaloid metabolic process / prenyltransferase activity
Similarity search - Function

Biological species

Aspergillus sp. (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Dan, Q. / Smith, J.L.

Funding support

United States, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2022
Title: Data Science-Driven Analysis of Substrate-Permissive Diketopiperazine Reverse Prenyltransferase NotF: Applications in Protein Engineering and Cascade Biocatalytic Synthesis of (-)-Eurotiumin A.
Authors: Kelly, S.P. / Shende, V.V. / Flynn, A.R. / Dan, Q. / Ye, Y. / Smith, J.L. / Tsukamoto, S. / Sigman, M.S. / Sherman, D.H.

History

Deposition	Feb 25, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 3, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 1, 2023	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Oct 25, 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	6vya.cif.gz	2.3 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	6vya_validation.pdf.gz	10.8 MB	Display	wwPDB validaton report
Full document	6vya_full_validation.pdf.gz	11.4 MB	Display
Data in XML	6vya_validation.xml.gz	403.2 KB	Display
Data in CIF	6vya_validation.cif.gz	506.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vy/6vya ftp://data.pdbj.org/pub/pdb/validation_reports/vy/6vya	HTTPS FTP

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Related structure data

Related structure data	6vy9C 4ld7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ld7-1 6vy9-2 6vy9-1 4ld7-4 4e0u-3 4ld7-3 5h3s-d 5dt5-1 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) 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

6vy9C

4ld7S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#201 - Sep 2016 Isoprene Synthase similarity (1)

Deposited unit

C: Deoxybrevianamide E synthase notF

A: Deoxybrevianamide E synthase notF

V: Deoxybrevianamide E synthase notF

E: Deoxybrevianamide E synthase notF

G: Deoxybrevianamide E synthase notF

B: Deoxybrevianamide E synthase notF

D: Deoxybrevianamide E synthase notF

F: Deoxybrevianamide E synthase notF

H: Deoxybrevianamide E synthase notF

I: Deoxybrevianamide E synthase notF

J: Deoxybrevianamide E synthase notF

K: Deoxybrevianamide E synthase notF

L: Deoxybrevianamide E synthase notF

M: Deoxybrevianamide E synthase notF

N: Deoxybrevianamide E synthase notF

O: Deoxybrevianamide E synthase notF

P: Deoxybrevianamide E synthase notF

Q: Deoxybrevianamide E synthase notF

R: Deoxybrevianamide E synthase notF

S: Deoxybrevianamide E synthase notF

T: Deoxybrevianamide E synthase notF

U: Deoxybrevianamide E synthase notF

W: Deoxybrevianamide E synthase notF

X: Deoxybrevianamide E synthase notF

hetero molecules

1.31 MDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: Deoxybrevianamide E synthase notF

A: Deoxybrevianamide E synthase notF

E: Deoxybrevianamide E synthase notF

G: Deoxybrevianamide E synthase notF

hetero molecules

defined by author
Evidence: gel filtration
218 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

V: Deoxybrevianamide E synthase notF

U: Deoxybrevianamide E synthase notF

W: Deoxybrevianamide E synthase notF

X: Deoxybrevianamide E synthase notF

hetero molecules

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

3

B: Deoxybrevianamide E synthase notF

D: Deoxybrevianamide E synthase notF

F: Deoxybrevianamide E synthase notF

H: Deoxybrevianamide E synthase notF

hetero molecules

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

4

I: Deoxybrevianamide E synthase notF

J: Deoxybrevianamide E synthase notF

K: Deoxybrevianamide E synthase notF

L: Deoxybrevianamide E synthase notF

hetero molecules

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

5

M: Deoxybrevianamide E synthase notF

N: Deoxybrevianamide E synthase notF

O: Deoxybrevianamide E synthase notF

P: Deoxybrevianamide E synthase notF

hetero molecules

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

6

Q: Deoxybrevianamide E synthase notF

R: Deoxybrevianamide E synthase notF

S: Deoxybrevianamide E synthase notF

T: Deoxybrevianamide E synthase notF

hetero molecules

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

Unit cell

Length a, b, c (Å)	157.893, 163.069, 167.857
Angle α, β, γ (deg.)	78.255, 65.051, 66.396
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain 'A'	A	32 - 181
1	2	1	chain 'A'	A	192 - 326
1	3	1	chain 'A'	A	349 - 447
1	4	1	chain 'A'	A	501
1	5	1	chain 'A'	A	601
2	1	1	chain 'B'	B	32 - 181
2	2	1	chain 'B'	B	192 - 326
2	3	1	chain 'B'	B	349 - 447
2	4	1	chain 'B'	B	501
2	5	1	chain 'B'	B	601
3	1	1	chain 'C'	C	32 - 181
3	2	1	chain 'C'	C	192 - 326
3	3	1	chain 'C'	C	349 - 447
3	4	1	chain 'C'	C	501
3	5	1	chain 'C'	C	601
4	1	1	chain 'D'	D	32 - 181
4	2	1	chain 'D'	D	192 - 326
4	3	1	chain 'D'	D	349 - 447
4	4	1	chain 'D'	D	501
4	5	1	chain 'D'	D	601
5	1	1	chain 'E'	E	32 - 181
5	2	1	chain 'E'	E	192 - 326
5	3	1	chain 'E'	E	349 - 447
5	4	1	chain 'E'	E	501
5	5	1	chain 'E'	E	601
6	1	1	chain 'F'	F	32 - 181
6	2	1	chain 'F'	F	192 - 326
6	3	1	chain 'F'	F	349 - 447
6	4	1	chain 'F'	F	501
6	5	1	chain 'F'	F	601
7	1	1	chain 'G'	G	32 - 181
7	2	1	chain 'G'	G	192 - 326
7	3	1	chain 'G'	G	349 - 447
7	4	1	chain 'G'	G	501
7	5	1	chain 'G'	G	601
8	1	1	chain 'H'	H	32 - 181
8	2	1	chain 'H'	H	192 - 326
8	3	1	chain 'H'	H	349 - 447
8	4	1	chain 'H'	H	501
8	5	1	chain 'H'	H	601
9	1	1	chain 'I'	I	32 - 181
9	2	1	chain 'I'	I	192 - 326
9	3	1	chain 'I'	I	349 - 447
9	4	1	chain 'I'	I	501
9	5	1	chain 'I'	I	601
10	1	1	chain 'J'	J	32 - 181
10	2	1	chain 'J'	J	192 - 326
10	3	1	chain 'J'	J	349 - 447
10	4	1	chain 'J'	J	501
10	5	1	chain 'J'	J	601
11	1	1	chain 'K'	K	32 - 181
11	2	1	chain 'K'	K	192 - 326
11	3	1	chain 'K'	K	349 - 447
11	4	1	chain 'K'	K	501
11	5	1	chain 'K'	K	601
12	1	1	chain 'L'	L	32 - 181
12	2	1	chain 'L'	L	192 - 326
12	3	1	chain 'L'	L	349 - 447
12	4	1	chain 'L'	L	501
12	5	1	chain 'L'	L	601
13	1	1	chain 'M'	M	32 - 181
13	2	1	chain 'M'	M	192 - 326
13	3	1	chain 'M'	M	349 - 447
13	4	1	chain 'M'	M	501
13	5	1	chain 'M'	M	601
14	1	1	chain 'N'	N	32 - 181
14	2	1	chain 'N'	N	192 - 326
14	3	1	chain 'N'	N	349 - 447
14	4	1	chain 'N'	N	501
14	5	1	chain 'N'	N	601
15	1	1	chain 'O'	O	32 - 181
15	2	1	chain 'O'	O	192 - 326
15	3	1	chain 'O'	O	349 - 447
15	4	1	chain 'O'	O	501
15	5	1	chain 'O'	O	601
16	1	1	chain 'P'	P	32 - 181
16	2	1	chain 'P'	P	192 - 326
16	3	1	chain 'P'	P	349 - 447
16	4	1	chain 'P'	P	501
16	5	1	chain 'P'	P	601
17	1	1	chain 'Q'	Q	32 - 181
17	2	1	chain 'Q'	Q	192 - 326
17	3	1	chain 'Q'	Q	349 - 447
17	4	1	chain 'Q'	Q	501
17	5	1	chain 'Q'	Q	601
18	1	1	chain 'R'	R	32 - 181
18	2	1	chain 'R'	R	192 - 326
18	3	1	chain 'R'	R	349 - 447
18	4	1	chain 'R'	R	501
18	5	1	chain 'R'	R	601
19	1	1	chain 'S'	S	32 - 181
19	2	1	chain 'S'	S	192 - 326
19	3	1	chain 'S'	S	349 - 447
19	4	1	chain 'S'	S	501
19	5	1	chain 'S'	S	601
20	1	1	chain 'T'	T	32 - 181
20	2	1	chain 'T'	T	192 - 326
20	3	1	chain 'T'	T	349 - 447
20	4	1	chain 'T'	T	501
20	5	1	chain 'T'	T	601
21	1	1	chain 'U'	U	32 - 181
21	2	1	chain 'U'	U	192 - 326
21	3	1	chain 'U'	U	349 - 447
21	4	1	chain 'U'	U	501
21	5	1	chain 'U'	U	601
22	1	1	chain 'V'	V	32 - 181
22	2	1	chain 'V'	V	192 - 326
22	3	1	chain 'V'	V	349 - 447
22	4	1	chain 'V'	V	501
22	5	1	chain 'V'	V	601
23	1	1	chain 'W'	W	32 - 181
23	2	1	chain 'W'	W	192 - 326
23	3	1	chain 'W'	W	349 - 447
23	4	1	chain 'W'	W	501
23	5	1	chain 'W'	W	601
24	1	1	chain 'X'	X	32 - 181
24	2	1	chain 'X'	X	192 - 326
24	3	1	chain 'X'	X	349 - 447
24	4	1	chain 'X'	X	501
24	5	1	chain 'X'	X	601

#1: Protein	... Deoxybrevianamide E synthase notF / Reverse prenyltransferase notF Mass: 53832.211 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus sp. (mold) / Strain: MF297-2 / Gene: notF / Production host: Escherichia coli (E. coli) References: UniProt: E0Y3X1, brevianamide F prenyltransferase (deoxybrevianamide E-forming)
#2: Chemical	... ChemComp-QRP / (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione / Brevianamide F / cyclo-L-Trp-L-Pro Mass: 283.325 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₁₆H₁₇N₃O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate Mass: 262.158 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₅H₁₂O₆P₂S / Feature type: SUBJECT OF INVESTIGATION
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: 2.78 Å³/Da / Density % sol: 55.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.9 Details: 11% w/v PEG 4000, 0.1 M MES pH 6.9, 0.2 M MgCl2, 1 mM brevianamide F, 1 mM dimethylallyl S-thiolodiphosphate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2019
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 2.99→49.13 Å / Num. obs: 274067 / % possible obs: 97.5 % / Redundancy: 3.5 % / B_iso Wilson estimate: 97.18 Å² / CC_1/2: 1 / Net I/σ(I): 7.3
Reflection shell	Resolution: 2.99→3.1 Å / Num. unique obs: 26465 / CC_1/2: 0.4

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4LD7

4ld7

Resolution: 3→49.13 Å / SU ML: 0.6493 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 44.7121

	R_factor	Num. reflection	% reflection
R_free	0.3083	1971	0.72 %
R_work	0.2649	-	-
obs	0.2652	272558	97.48 %

Solvent computation

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

Displacement parameters

B_iso mean: 109.63 Å²

Refinement step

Cycle: LAST / Resolution: 3→49.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	76752	0	0	0	76752

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0093	79248
X-RAY DIFFRACTION	f_angle_d	1.1684	107856
X-RAY DIFFRACTION	f_chiral_restr	0.056	11184
X-RAY DIFFRACTION	f_plane_restr	0.0096	13752
X-RAY DIFFRACTION	f_dihedral_angle_d	16.559	10296

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 (%)
3-3.07	0.5038	134	0.5126	18026	X-RAY DIFFRACTION	90.71
3.07-3.15	0.5396	133	0.4848	19395	X-RAY DIFFRACTION	98.01
3.15-3.25	0.4784	148	0.4385	19447	X-RAY DIFFRACTION	98.13
3.25-3.35	0.4367	133	0.3892	19536	X-RAY DIFFRACTION	98.22
3.35-3.47	0.3702	142	0.3541	19438	X-RAY DIFFRACTION	98.21
3.47-3.61	0.3769	146	0.3342	19460	X-RAY DIFFRACTION	98.34
3.61-3.77	0.4359	137	0.3795	19466	X-RAY DIFFRACTION	98.07
3.77-3.97	0.3405	146	0.2898	19522	X-RAY DIFFRACTION	98.4
3.97-4.22	0.273	142	0.248	19472	X-RAY DIFFRACTION	98.41
4.22-4.55	0.3134	140	0.219	19557	X-RAY DIFFRACTION	98.4
4.55-5	0.2579	146	0.2095	19467	X-RAY DIFFRACTION	98.28
5-5.73	0.2438	136	0.2112	19387	X-RAY DIFFRACTION	97.94
5.73-7.21	0.2921	144	0.2475	19512	X-RAY DIFFRACTION	98.25
7.21-49.13	0.2298	144	0.1843	18902	X-RAY DIFFRACTION	95.38

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