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- PDB-8zrl: Crystal structure of methanol dehydrogenase2 from Bacillus methan... -

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Basic information

Entry
Database: PDB / ID: 8zrl
TitleCrystal structure of methanol dehydrogenase2 from Bacillus methanolicus complexed with an inhibitor
ComponentsNAD-dependent methanol dehydrogenase
KeywordsOXIDOREDUCTASE / Methanol dehydrogenase / TypeIII alcohol dehydrogenase
Function / homology
Function and homology information


methanol dehydrogenase / methanol dehydrogenase (NAD+) activity / metal ion binding
Similarity search - Function
Iron-type alcohol dehydrogenase-like / : / Fe-containing alcohol dehydrogenase family, C-terminal / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / : / NAD-dependent methanol dehydrogenase
Similarity search - Component
Biological speciesBacillus methanolicus MGA3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMa, B.D. / Zhang, M.J. / Kong, X.D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0911000 China
CitationJournal: J.Biol.Chem. / Year: 2025
Title: ADP-ribose is a competitive inhibitor of methanol dehydrogenases from Bacillus methanolicus.
Authors: Ma, B.D. / Li, J.Y. / Xu, J.H. / Yu, T. / Kong, X.D.
History
DepositionJun 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent methanol dehydrogenase
B: NAD-dependent methanol dehydrogenase
C: NAD-dependent methanol dehydrogenase
D: NAD-dependent methanol dehydrogenase
E: NAD-dependent methanol dehydrogenase
F: NAD-dependent methanol dehydrogenase
G: NAD-dependent methanol dehydrogenase
H: NAD-dependent methanol dehydrogenase
I: NAD-dependent methanol dehydrogenase
J: NAD-dependent methanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)424,26130
Polymers418,11810
Non-polymers6,14320
Water12,827712
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.571, 204.410, 258.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
NAD-dependent methanol dehydrogenase


Mass: 41811.809 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus methanolicus MGA3 (bacteria) / Strain: MGA3 / ATCC 53907 / Gene: mdh2, BMMGA3_03335 / Production host: Escherichia coli (E. coli) / References: UniProt: I3E2P9, methanol dehydrogenase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium formate,0.1 M Bistris propane pH6.0 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.6→86.05 Å / Num. obs: 136650 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.915 / Rmerge(I) obs: 0.355 / Rpim(I) all: 0.147 / Rrim(I) all: 0.294 / Χ2: 2.18 / Net I/σ(I): 14.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.629 / Num. unique obs: 6650 / CC1/2: 0.812

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→79.51 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 6804 4.99 %
Rwork0.1933 --
obs0.1956 136469 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→79.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28470 0 370 712 29552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00829332
X-RAY DIFFRACTIONf_angle_d1.42139832
X-RAY DIFFRACTIONf_dihedral_angle_d10.5924045
X-RAY DIFFRACTIONf_chiral_restr0.114732
X-RAY DIFFRACTIONf_plane_restr0.0145106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.32382420.25694258X-RAY DIFFRACTION100
2.63-2.660.33132110.24064258X-RAY DIFFRACTION100
2.66-2.690.2982170.23844324X-RAY DIFFRACTION100
2.69-2.730.2822240.23044245X-RAY DIFFRACTION100
2.73-2.760.30742160.22924280X-RAY DIFFRACTION100
2.76-2.80.29522320.22884277X-RAY DIFFRACTION100
2.8-2.840.29822210.25414287X-RAY DIFFRACTION100
2.84-2.880.32852070.25984305X-RAY DIFFRACTION100
2.88-2.930.28952570.24224208X-RAY DIFFRACTION100
2.93-2.980.33152340.23214331X-RAY DIFFRACTION100
2.98-3.030.25912210.22294265X-RAY DIFFRACTION100
3.03-3.080.29542340.22314293X-RAY DIFFRACTION100
3.08-3.140.27442420.22474252X-RAY DIFFRACTION100
3.14-3.210.28812570.22534319X-RAY DIFFRACTION100
3.21-3.280.29352330.23194235X-RAY DIFFRACTION100
3.28-3.350.26582100.23014369X-RAY DIFFRACTION100
3.35-3.440.26611940.2254303X-RAY DIFFRACTION100
3.44-3.530.25952380.20724312X-RAY DIFFRACTION100
3.53-3.630.25712350.19714329X-RAY DIFFRACTION100
3.63-3.750.25512410.19324261X-RAY DIFFRACTION100
3.75-3.880.24982250.18164306X-RAY DIFFRACTION100
3.88-4.040.21892270.17254333X-RAY DIFFRACTION100
4.04-4.220.19042470.164325X-RAY DIFFRACTION100
4.22-4.450.18642210.15184366X-RAY DIFFRACTION100
4.45-4.720.16122230.1494341X-RAY DIFFRACTION100
4.72-5.090.19082180.15124371X-RAY DIFFRACTION100
5.09-5.60.2212160.17624431X-RAY DIFFRACTION100
5.6-6.410.22842170.17824424X-RAY DIFFRACTION100
6.41-8.080.18382030.15444482X-RAY DIFFRACTION100
8.08-79.510.20882410.18144575X-RAY DIFFRACTION98

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