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- PDB-9rui: Apo state of the CdmB methyltransferase involved in the anaerobic... -

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Basic information

Entry
Database: PDB / ID: 9rui
TitleApo state of the CdmB methyltransferase involved in the anaerobic dehalogenation of haloalkanes
ComponentsCdmB from Acetobacterium malicum subsp. dehalogenans
KeywordsTRANSFERASE / Chloromethane conversion / acetogenesis / anaerobic bacteria / dehalogenation / methyl-transfer
Function / homologyChem-ETE / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION
Function and homology information
Biological speciesAcetobacterium malicum subsp. dehalogenans DSM 11527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsWagner, T. / Lemaire, O.N.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)KU 3768/3-1 Germany
CitationJournal: Nat Commun / Year: 2026
Title: Identification and characterisation of an elusive bacterial enzyme system for chloromethane dehalogenation.
Authors: Bernhardt, J. / Hofmann, L.K.R. / Klemm, P. / Paczia, N. / Lemaire, O.N. / Vuilleumier, S. / Wagner, T. / Kurth, J.M.
History
DepositionJul 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CdmB from Acetobacterium malicum subsp. dehalogenans
B: CdmB from Acetobacterium malicum subsp. dehalogenans
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,21152
Polymers96,3062
Non-polymers3,90550
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12830 Å2
ΔGint38 kcal/mol
Surface area31590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.511, 85.792, 155.797
Angle α, β, γ (deg.)90.00, 99.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-795-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CdmB from Acetobacterium malicum subsp. dehalogenans


Mass: 48153.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: /
Source: (gene. exp.) Acetobacterium malicum subsp. dehalogenans DSM 11527 (bacteria)
Strain: DSM 11527 / Tissue: / / Cell: / / Cell line: / / Gene: ACIUZZ_RS16855 / Organ: / / Variant: / / Plasmid: pET-30a
Details (production host): Insertion of a N-terminal StrepII tag
Cell (production host): / / Cell line (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Tissue (production host): / / Variant (production host): /

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Non-polymers , 9 types, 552 molecules

#2: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.46 % / Description: Transparent hexagonal plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: The protein was crystallized at 17.6 mg/ml in 25 mM Tris-HCl pH 7.6, 10% v/v glycerol, 0.1 mM ZnCl2, and 2 mM dithiothreitol. Initial screening was performed on a 96-Well MRC 2-Drop ...Details: The protein was crystallized at 17.6 mg/ml in 25 mM Tris-HCl pH 7.6, 10% v/v glycerol, 0.1 mM ZnCl2, and 2 mM dithiothreitol. Initial screening was performed on a 96-Well MRC 2-Drop polystyrene Crystallization Plate (SWISSCI). From the initial hit, crystallization was further refined and performed aerobically at 20 degrees Celsius using the sitting drop method on CombiClover Jr crystallization plates (Molecular Dimensions). The reservoir chamber was filled with 100 ul of the crystallization solution containing: 50 % (v/v) Polyethylene glycol 200, 100 mM Sodium Potassium phosphate pH 6.2, and 200 mM Sodium chloride. The crystallization drop was formed by spotting 0.9 ul of purified protein with 0.9 ul of precipitant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.57→153.86 Å / Num. obs: 82269 / % possible obs: 90.6 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.025 / Rrim(I) all: 0.066 / Net I/σ(I): 15.7
Reflection shellResolution: 1.57→1.72 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4113 / CC1/2: 0.53 / Rpim(I) all: 0.498 / Rrim(I) all: 1.329 / % possible all: 57.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→27.88 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.07 / Stereochemistry target values: ML
Details: The model was improved with COOT and refined with PHENIX_refine. Models were refined by applying translational-libration-screw and by adding riding hydrogens. The model has been deposited without hydrogen atoms.
RfactorNum. reflection% reflection
Rfree0.1953 4225 5.14 %
Rwork0.1733 --
obs0.1744 82182 65.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.47 Å2
Refinement stepCycle: LAST / Resolution: 1.57→27.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6638 0 246 502 7386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087078
X-RAY DIFFRACTIONf_angle_d19517
X-RAY DIFFRACTIONf_dihedral_angle_d15.7742604
X-RAY DIFFRACTIONf_chiral_restr0.0591028
X-RAY DIFFRACTIONf_plane_restr0.0081201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.590.192120.360714X-RAY DIFFRACTION0
1.59-1.610.082620.25668X-RAY DIFFRACTION2
1.61-1.630.445160.268156X-RAY DIFFRACTION4
1.63-1.650.1934130.2582387X-RAY DIFFRACTION10
1.65-1.670.35480.2692682X-RAY DIFFRACTION17
1.67-1.690.2784590.2785968X-RAY DIFFRACTION25
1.69-1.720.284680.25411239X-RAY DIFFRACTION31
1.72-1.740.2409850.25671388X-RAY DIFFRACTION36
1.74-1.770.3244720.25121711X-RAY DIFFRACTION43
1.77-1.80.23871200.25861884X-RAY DIFFRACTION48
1.8-1.830.25891130.24922182X-RAY DIFFRACTION55
1.83-1.860.21571380.25452274X-RAY DIFFRACTION58
1.86-1.90.25511260.23882531X-RAY DIFFRACTION63
1.9-1.940.22741260.23592716X-RAY DIFFRACTION68
1.94-1.980.24461540.2282972X-RAY DIFFRACTION74
1.98-2.020.25022060.22473037X-RAY DIFFRACTION78
2.02-2.070.2751890.20923430X-RAY DIFFRACTION87
2.07-2.130.25962100.19773710X-RAY DIFFRACTION93
2.13-2.190.22192180.19863813X-RAY DIFFRACTION97
2.19-2.260.2582090.18513848X-RAY DIFFRACTION97
2.26-2.350.21672280.17993859X-RAY DIFFRACTION98
2.35-2.440.19321930.17633912X-RAY DIFFRACTION98
2.44-2.550.18741690.1713790X-RAY DIFFRACTION94
2.55-2.680.20821840.16913908X-RAY DIFFRACTION97
2.68-2.850.20871940.16383935X-RAY DIFFRACTION99
2.85-3.070.17942620.16383916X-RAY DIFFRACTION99
3.07-3.380.19191880.16373916X-RAY DIFFRACTION98
3.38-3.870.16772250.14463801X-RAY DIFFRACTION95
3.87-4.870.14832220.13073958X-RAY DIFFRACTION99
4.87-27.880.17791960.18063952X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.13740.2102-0.27590.4323-0.26850.7734-0.0407-0.27380.4360.2322-0.031-0.205-0.09840.3872-0.07480.17920.005-0.15480.2325-0.17660.571833.019724.29816.0574
22.35250.5202-0.99771.1123-0.77551.3845-0.056-0.20480.00460.00870.0434-0.11360.18860.12890.01760.1720.065-0.07430.1121-0.0470.198416.80386.574517.3157
32.40320.5245-1.10991.6523-0.69751.01490.0008-0.1998-0.00480.2150.00040.10.0059-0.1094-0.0010.20440.0578-0.04250.2453-0.06930.09645.50456.154926.7606
40.71130.03050.04020.7515-0.07720.5594-0.09-0.12080.5330.13010.0856-0.0498-0.0579-0.06890.01780.12780.0552-0.05830.1218-0.10170.353411.081825.19412.2834
51.42820.13160.69440.9627-0.4092.49180.1702-0.13960.01010.2688-0.2081-0.08950.26290.28630.03920.4214-0.02780.02150.3516-0.00810.101423.9203-10.487853.212
60.4623-0.39890.74691.825-0.43782.1071-0.0061-0.14950.0330.2138-0.03930.40750.1322-0.41120.04080.3032-0.02190.08470.3636-0.06190.167.3369-7.697243.7822
71.8785-0.02050.44131.2263-0.93482.26480.1597-0.1895-0.26820.2344-0.02990.25850.7057-0.2892-0.10480.737-0.13460.08490.3621-0.0230.223110.4415-24.886752.4321
80.9261-0.03960.21170.5597-0.87381.53350.0701-0.4761-0.31140.1132-0.0732-0.08120.50520.28710.04051.0038-0.0021-0.0940.5850.1170.091827.5363-24.545467.3514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -9 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 203 )
4X-RAY DIFFRACTION4chain 'A' and (resid 204 through 419 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 133 )
6X-RAY DIFFRACTION6chain 'B' and (resid 134 through 203 )
7X-RAY DIFFRACTION7chain 'B' and (resid 204 through 327 )
8X-RAY DIFFRACTION8chain 'B' and (resid 328 through 419 )

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