28JB | pdb_000028jb

Structure of DarM methyltransferase in complex with SAH

PDB DOI: https://doi.org/10.2210/pdb28JB/pdb

Classification: TRANSFERASE
Organism(s): Micromonospora rubida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-02-03 Released: 2026-11-04
Deposition Author(s): Kolling, D., Koehnke, J.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.192 (Depositor), 0.191 (DCC)
R-Value Work:
0.176 (Depositor), 0.176 (DCC)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Discovery and Biosynthetic Characterization of Darumycins Expand the Chemical Space of Sesterterpene Antibiotics

Bratiichuk, D., Kolling, D., Redzic, I., Stierhof, M., Fries, F., Zapp, J., Muller, R., Myronovskyi, M., Koehnke, J., Luzhetskyy, A.

(2026) JACS Au 6: 4944-4955

DOI: https://doi.org/10.1021/jacsau.6c00499

Macromolecule Content

Total Structure Weight: 31.55 kDa
Atom Count: 2,158
Modeled Residue Count: 263
Deposited Residue Count: 291
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DarM	A	291	Micromonospora rubida	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH 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]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.192 (Depositor), 0.191 (DCC)
R-Value Work: 0.176 (Depositor), 0.176 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.722	α = 90
b = 67.502	β = 90
c = 91.858	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Germany	--

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release