9RUL | pdb_00009rul

CdmB methyltransferase involved in the anaerobic dehalogenation of haloalkanes soaked with dichloromethane

• PDB DOI: https://doi.org/10.2210/pdb9RUL/pdb

• Classification: TRANSFERASE
• Organism(s): Acetobacterium malicum subsp. dehalogenans DSM 11527
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-04 Released: 2026-06-03 
• Deposition Author(s): Wagner, T., Lemaire, O.N.
• Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.191 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Identification and characterisation of a long-elusive bacterial enzyme system for chloromethane conversion

Bernhardt, J., Hofmann, L.K.R., Klemm, P., Paczia, N., Lemaire, O.N., Vuilleumier, S., Wagner, T., Kurth, J.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 101.88 kDa 
• Atom Count: 7,496 
• Modeled Residue Count: 838 
• Deposited Residue Count: 858 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CdmB from Acetobacterium malicum subsp. dehalogenans	A, B	429	Acetobacterium malicum subsp. dehalogenans DSM 11527	Mutation(s): 0  Gene Names: ACIUZZ_RS16855

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ETE	C [auth A]	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C9 H20 O5 ZNYRFEPBTVGZDN-UHFFFAOYSA-N
PG4	L [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	EB [auth B], FA [auth A], G [auth A], H [auth A], K [auth A], KA [auth A], O [auth A], P [auth A], PA [auth A], Q [auth A], RA [auth A], Z [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	VA [auth A], WA [auth A], XA [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	AB [auth B], BB [auth B], EA [auth A], GA [auth A], J [auth A], JA [auth A], SA [auth A], TB [auth B], U [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
A1JJJ( Subject of Investigation/LOI)	CA [auth A], DA [auth A], MB [auth B]	dichloromethane C H2 Cl2 YMWUJEATGCHHMB-UHFFFAOYSA-N
EDO	AA [auth A], BA [auth A], CB [auth B], D [auth A], DB [auth B], E [auth A], F [auth A], FB [auth B], GB [auth B], HA [auth A], HB [auth B], I [auth A], IA [auth A], IB [auth B], JB [auth B], KB [auth B], LA [auth A], LB [auth B], M [auth A], MA [auth A], N [auth A], NA [auth A], NB [auth B], OA [auth A], OB [auth B], PB [auth B], QA [auth A], QB [auth B], R [auth A], RB [auth B], S [auth A], SB [auth B], T [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], ZA [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	TA [auth A], UA [auth A], UB [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	VB [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	YA [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.191 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.567	α = 90
b = 86.061	β = 99.29
c = 156.272	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Wagner, T., Lemaire, O.N.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
German Research Foundation (DFG)	Germany	KU 3768/3-1

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release