9VT8 | pdb_00009vt8

Crystal structure of SmiF bound with a substrate peptide and DMASPP

PDB DOI: https://doi.org/10.2210/pdb9VT8/pdb

Classification: TRANSFERASE
Organism(s): Scytonema millei, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-07-10 Released: 2026-06-24
Deposition Author(s): Inoue, S., Hamada, K., Goto, Y., Suga, H., Sengoku, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.264 (Depositor), 0.263 (DCC)
R-Value Work:
0.205 (Depositor), 0.207 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Rapid screening platform for peptide prenyltransferases to diversify pseudo-natural prenylated peptides

(null) Nat Catal

Macromolecule Content

Total Structure Weight: 35.03 kDa
Atom Count: 2,314
Modeled Residue Count: 280
Deposited Residue Count: 300
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SmiF	A	293	Scytonema millei	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIS-PRO-TRP-GLY-VAL	B	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DST (Subject of Investigation/LOI) Query on DST Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DIMETHYLALLYL S-THIOLODIPHOSPHATE C₅ H₁₂ O₆ P₂ S ZWFWSISPSBLNGO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.264 (Depositor), 0.263 (DCC)
R-Value Work: 0.205 (Depositor), 0.207 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.2	α = 90
b = 61.95	β = 90
c = 118.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2026-06-24
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.