PDB-9vtc: Crystal structure of DciF bound with DMASPP

ID or keywords:

Entry

Database: PDB / ID: 9vtc

Title

Crystal structure of DciF bound with DMASPP

Components

DciF

Keywords

TRANSFERASE / Peptide Prenyltransferase

Function / homology

DIMETHYLALLYL S-THIOLODIPHOSPHATE

Function and homology information

Biological species

Dolichospermum circinale (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Ito, S. / Hamada, K. / Inoue, S. / Suga, H. / Goto, Y. / Sengoku, T.

Funding support

Japan, 1items

Citation

Journal: Nat Catal
Title: Rapid screening platform for peptide prenyltransferases to diversify pseudo-natural prenylated peptides
Authors: Inoue, S.

History

Deposition	Jul 10, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 24, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9vtc.cif.gz	585.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9vtc.ent.gz	401.2 KB	Display	PDB format
PDBx/mmJSON format	9vtc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vt/9vtc ftp://data.pdbj.org/pub/pdb/validation_reports/vt/9vtc	HTTPS FTP

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Related structure data

Related structure data	9vt8C 9vt9C 9vtaC 9vtbC 9vtdC 9vteC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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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

A: DciF

B: DciF

C: DciF

D: DciF

hetero molecules

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

1

A: DciF

hetero molecules

defined by author
34.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DciF

hetero molecules

defined by author
34.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: DciF

hetero molecules

defined by author
34.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: DciF

hetero molecules

defined by author
34.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.670, 88.730, 93.910
Angle α, β, γ (deg.)	90.000, 104.050, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	DciF Mass: 33661.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Uniparc:UPI000413C8F1 / Source: (gene. exp.) Dolichospermum circinale (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 778 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate Mass: 262.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₁₂O₆P₂S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.83 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris, PEGMME5000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 20, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.85→49.75 Å / Num. obs: 97305 / % possible obs: 99.96 % / Redundancy: 81.5 % / B_iso Wilson estimate: 16.31 Å² / CC_1/2: 0.996 / Net I/σ(I): 10.67
Reflection shell	Resolution: 1.85→1.916 Å / Num. unique obs: 9679 / CC_1/2: 0.524

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.85→49.75 Å / SU ML: 0.2348 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.3004
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2429	1999	2.05 %
R_work	0.1929	95281	-
obs	0.1939	97280	99.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 27.05 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→49.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9319	0	142	764	10225

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0041	9658
X-RAY DIFFRACTION	f_angle_d	0.8171	13022
X-RAY DIFFRACTION	f_chiral_restr	0.0648	1444
X-RAY DIFFRACTION	f_plane_restr	0.0057	1652
X-RAY DIFFRACTION	f_dihedral_angle_d	21.5735	1318

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 (%)
1.85-1.9	0.3493	142	0.3371	6761	X-RAY DIFFRACTION	99.94
1.9-1.95	0.3539	142	0.3145	6748	X-RAY DIFFRACTION	100
1.95-2	0.321	142	0.2806	6815	X-RAY DIFFRACTION	99.97
2-2.07	0.2894	142	0.2406	6765	X-RAY DIFFRACTION	100
2.07-2.14	0.2721	143	0.2057	6776	X-RAY DIFFRACTION	99.94
2.14-2.23	0.2483	143	0.1984	6822	X-RAY DIFFRACTION	100
2.23-2.33	0.2691	141	0.1917	6760	X-RAY DIFFRACTION	99.97
2.33-2.45	0.2622	143	0.1879	6778	X-RAY DIFFRACTION	99.97
2.45-2.61	0.2274	143	0.1858	6807	X-RAY DIFFRACTION	100
2.61-2.81	0.2493	143	0.1814	6804	X-RAY DIFFRACTION	99.99
2.81-3.09	0.2571	143	0.1851	6811	X-RAY DIFFRACTION	99.97
3.09-3.54	0.2179	144	0.1669	6838	X-RAY DIFFRACTION	99.99
3.54-4.46	0.1878	143	0.1483	6856	X-RAY DIFFRACTION	100
4.46-49.75	0.1876	145	0.1653	6940	X-RAY DIFFRACTION	99.82

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	0.79028736087	-0.0839710292294	-0.249911908321	3.7994512542	0.324258672196	1.51455289338	-0.00675985533614	-0.218215542694	-0.0699599904429	0.508486447524	0.0576179216307	0.0553991930418	-0.448087634075	-0.175170522267	0.0226148301832	0.283679804748	-0.0315439441186	0.0185733943214	0.0163344955972	-0.0288617887963	0.049296462263	2.86988438097	13.3793448466	12.3759635806
2	6.99427693346	8.39775705059	-0.794547677437	1.99997866291	-1.59650899257	4.48938859194	-0.91663469897	-0.0495421128868	-0.539464684554	0.0500275656385	0.507837115562	0.53481714578	-0.387825620619	-0.421030548228	0.442318753881	0.438945233743	0.0721570719966	0.0939127527764	0.568544408865	-0.0463318978869	0.426759047616	-7.04456260419	15.2293677003	0.253011748559
3	1.24434080572	-0.258389346821	0.774510095492	1.55338494183	-0.125716508033	2.03388100472	0.000730697048834	0.106522306351	0.0736670271779	0.151067442698	-0.0559431297272	-0.0662879563825	-0.195281142867	0.0902686941416	0.0466547253666	0.253212289572	-0.010306413245	0.0480557315373	0.0564484602531	0.0096948493998	0.0814939103507	12.9349448687	29.0944034179	-39.9112732047
4	1.63072966844	-0.649011653165	0.0962007183801	1.67243404583	0.353975337728	2.33019322578	-0.056774236392	0.224746352612	0.188092860192	0.615739176951	-0.144377908082	-0.0376033521959	0.0308067247583	0.516653008285	-0.232636693604	0.381057244075	0.0140905188151	0.0424181790421	0.0467806275662	-0.0270396669743	0.0318461104714	13.1458354929	15.0143837775	-27.5803684665
5	0.629959419375	0.303077331472	0.247788966955	1.57214862944	-0.0493270687712	1.63367437064	0.0153553417132	0.0682709782	0.0031838372064	-0.129318363294	-0.0065699946047	-0.0285428862216	0.00356116259694	0.0145875033224	-0.00371404677148	0.217781501496	0.00523712998615	0.0593516315986	0.0674178771348	-0.0191131431698	0.0404273641107	8.52807029688	9.83779157832	-48.233910104
6	0.946904071602	0.0268364115593	-0.172311411619	1.93676247753	-0.213312058126	1.52935231385	-0.0532728055599	0.166223412169	-0.022754865205	-0.37559129193	0.0996564522794	0.0689401495914	-0.181947421683	0.0720252075095	-0.0486407846819	0.327282162919	-0.00458680151808	0.0173816911937	0.0956406420964	0.0363188069232	0.0817870567374	4.55699022019	26.3921139588	-56.774726263
7	1.99993050932	-3.69443888608	-0.295132838365	4.73826433378	3.35857467556	4.34915825808	-0.0705023289154	-0.253291993179	-0.18504398958	-0.537259145629	0.107724069585	-0.85031765883	-0.0843242453395	1.15194469177	-0.035547833711	0.172709396826	0.00675510919172	0.188779477805	0.404789308849	0.148532822313	0.374157788081	18.0792902351	28.87249703	-49.1076041689
8	1.95334041145	0.37500775256	0.799312638904	3.25597386219	0.0850011226539	2.82924070339	0.175942670655	-0.496632844094	0.199475839038	0.882054950361	-0.515757859292	-0.0421953941839	0.277806933983	-0.314671467225	0.236017275317	0.410327435616	-0.113556604711	-0.00381007997283	0.264087348344	-0.0517764833281	0.249682113932	35.4767403173	32.8316975809	10.4935251154
9	2.15032622027	1.32951970455	0.958391006877	4.2254847639	0.63940223716	2.72666384259	-0.0259154074328	0.0679748814207	0.0721600178815	-0.303281409615	-0.21350344819	0.140814437511	-0.0137324738096	-0.0916379337716	0.122630689955	0.199453522937	0.0289115634955	0.025321892879	0.0932529943226	-0.0137264831264	0.176933859688	31.5374641351	26.5822185163	-8.13923006951
10	1.99997849463	-2.66886908257	8.5176797069	5.43654028061	-5.53664478141	1.99994872896	0.191854464496	-0.0163317756098	-2.60833794971	0.34792678933	0.865004917246	0.0999719543803	0.551506338496	0.448191904064	-1.06873344778	0.402953354331	0.0823710570185	-0.0818840923164	0.627333412922	0.183851513445	0.822468413554	42.3089752926	40.6025578693	-1.56682145598
11	3.43436699358	-3.33314334162	-2.31756591486	3.2407841712	2.17436441528	2.28553306093	-0.182182456859	-0.0648968932039	-0.491889533452	0.228752708381	-0.0332941953802	0.413815575575	0.0531835790299	-0.228889509882	0.211650472271	0.239036792414	-0.0343767201401	-0.047815767367	0.0908041440918	-0.00605861066687	0.204624829485	43.6070608353	-14.2851046524	-38.411182666
12	0.926820515394	0.226690406568	-0.570525369416	3.09504530164	-0.235838614338	4.30358673865	0.13639625264	-0.0538630851591	-0.0512372774937	0.251876117665	-0.0336123877327	0.154464487588	-0.0355527944599	-0.244252294939	-0.0715904044427	0.13077469944	-0.0470205884712	-0.0412524687807	0.0956663471233	0.0262583989294	0.12758213355	49.1393399855	-5.16538783869	-39.2334832449
13	9.37858949012	-4.73492106444	-1.32728188011	5.58246727475	1.38281079016	2.84906542389	-0.128787998862	-0.482838408364	0.394247021624	0.771115043885	0.0601893100952	0.208174747962	-0.323187855693	-0.0116023788425	0.00913549180389	0.386565659968	-0.039805584245	0.0448038310794	0.124102583449	0.00316135701015	0.118111490334	50.9737103894	2.00476810612	-26.2760485647
14	6.51964018034	-1.69172213468	1.82900663535	1.55568432699	-1.37063361205	1.94696646718	-0.0234696837875	-0.46604064468	0.065575581653	0.065291063305	0.0320913703363	-0.0152357843697	-0.0437814118226	-0.0362579544299	-0.0261110491254	0.260892119391	-0.0305895989348	0.00267521722004	0.151771301796	-0.00820946811934	0.0676821849334	57.6652588271	10.6793242795	-31.6683324877
15	0.929258385191	-0.500827261756	0.462290686722	2.27205169526	-0.691514971598	1.72641795719	-0.0157272252589	-0.00223469432342	-0.0370031727652	-0.0793286175256	0.00475896021118	0.128428817162	-0.176376892912	0.0037676032597	0.005036245496	0.113618133041	-0.00807756767988	-0.026392804058	0.0464683469104	-0.00356746834359	0.107400671507	50.6206176608	12.0569471429	-43.8522548373
16	1.14271946036	0.159944122472	-0.0493312848206	1.53867335086	-0.641154157679	0.935484567239	-0.0562757770997	0.0780230289709	0.0434351293684	-0.373736438954	0.0184563508046	0.173139655418	-0.13029946315	-0.0797199874133	0.00474779753261	0.298496539954	0.02469198414	-0.0791463302042	0.0755593700078	-0.010992773998	0.12757533121	45.9188041309	11.3012332404	-60.082342923
17	1.21420316537	-0.631129170924	0.191059556353	2.99371057297	-0.507007859598	2.8420199833	0.0978177672318	0.0628442296556	-0.180064528344	-0.584300458393	-0.0850152687347	0.259350156111	0.115948039716	-0.172769057777	-0.0321065961633	0.302175043151	0.00293358427877	-0.0575459636151	0.0876761567235	-0.0156183872712	0.135178449722	47.4883519496	-4.96596798327	-58.548501558
18	1.9999640077	-8.63107602909	-3.64256926403	1.9999768852	9.44509609674	6.98395391558	0.594393199457	-0.564346583149	1.1400746377	1.34615439778	0.716420879577	0.885862428631	-1.32831501528	0.894130388961	-1.33907029222	0.605662262539	-0.0922681374611	0.336610901524	0.863041859657	-0.0953657265836	0.50652106796	39.3534556546	-6.44257886155	-45.4056180165
19	0.857834571458	-0.0552043708658	0.400906679682	1.4922508136	0.0342684899455	2.65089185778	0.0309884571344	0.0184101015013	-0.0150768014111	-0.174680764858	-0.00832813671121	0.0194885960562	-0.133374618429	-0.0648209952203	-0.00704949963809	0.177957729681	0.0207037430828	0.0339273934804	0.02474508282	0.00315171924127	0.0808304285258	1.05039065908	15.3959190689	-6.66136836083
20	1.346410216	0.616933936995	-0.330937769025	2.50743926158	-0.57000081325	1.63074328165	-0.0631968383157	0.052871158718	-0.102290788491	-0.421269263834	0.0379846088078	-0.0913585019258	0.209922084284	0.043678891661	0.00537900574718	0.212473128981	0.00299104591201	0.0293078577894	0.0730927369581	-0.00574448742223	0.0582704375547	4.05066340374	1.32835099661	-12.5223633264
21	0.412481724367	-0.0516967028889	0.01872863356	1.88287873522	-0.478636033809	1.7354784172	0.00210002083666	-0.0502256041593	-0.0408206096843	0.166326473646	-0.0246057566944	-0.0182899556566	0.114377933127	0.054001760999	0.0100871017749	0.12820117051	-0.019545292518	0.0187824896568	0.0318340679741	0.00183648638806	0.0509186385558	2.07900662039	-5.14426479256	7.47139613231

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 238 through 288 )	A	A	238 - 288	231 - 281
2	2	chain 'A' and (resid 289 through 289 )	A	A	289	282
3	3	chain 'B' and (resid 6 through 72 )	B	E	6 - 72	1 - 67
4	4	chain 'B' and (resid 73 through 108 )	B	E	73 - 108	68 - 103
5	5	chain 'B' and (resid 109 through 237 )	B	E	109 - 237	104 - 232
6	6	chain 'B' and (resid 238 through 288 )	B	E	238 - 288	233 - 283
7	7	chain 'B' and (resid 289 through 289 )	B	E	289	284
8	8	chain 'C' and (resid 9 through 139 )	C	J	9 - 139	1 - 129
9	9	chain 'C' and (resid 140 through 288 )	C	J	140 - 288	130 - 278
10	10	chain 'C' and (resid 289 through 289 )	C	J	289	279
11	11	chain 'D' and (resid 5 through 20 )	D	N	5 - 20	5 - 20
12	12	chain 'D' and (resid 21 through 72 )	D	N	21 - 72	21 - 72
13	13	chain 'D' and (resid 73 through 88 )	D	N	73 - 88	73 - 88
14	14	chain 'D' and (resid 89 through 108 )	D	N	89 - 108	89 - 108
15	15	chain 'D' and (resid 109 through 190 )	D	N	109 - 190	109 - 190
16	16	chain 'D' and (resid 191 through 237 )	D	N	191 - 237	191 - 237
17	17	chain 'D' and (resid 238 through 288 )	D	N	238 - 288	238 - 288
18	18	chain 'D' and (resid 289 through 289 )	D	N	289	289
19	19	chain 'A' and (resid 8 through 72 )	A	A	8 - 72	1 - 65
20	20	chain 'A' and (resid 73 through 139 )	A	A	73 - 139	66 - 132
21	21	chain 'A' and (resid 140 through 237 )	A	A	140 - 237	133 - 230

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