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- PDB-9jav: Crystal structure of NAD-dependent methanol dehydrogenase 2 from ... -

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Basic information

Entry
Database: PDB / ID: 9jav
TitleCrystal structure of NAD-dependent methanol dehydrogenase 2 from Bacillus methanolicus MGA3 in complex with NAD+
ComponentsNAD-dependent methanol dehydrogenase
KeywordsOXIDOREDUCTASE / methanol 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 / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent methanol dehydrogenase
Similarity search - Component
Biological speciesBacillus methanolicus MGA3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKong, X.D. / Ma, B.D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0911000 China
CitationJournal: To Be Published
Title: Crystal structure of NAD-dependent methanol dehydrogenase 2 from Bacillus methanolicus MGA3 in complex with NAD+
Authors: Kong, X.D. / Ma, B.D.
History
DepositionAug 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)425,09430
Polymers418,11810
Non-polymers6,97520
Water20,4111133
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)83.520, 204.100, 258.070
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) / 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1133 / 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: 53.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium formate, 0.1 M Bis Tris propane, pH 6.5, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.6→59.92 Å / Num. obs: 136361 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.242 / Rpim(I) all: 0.068 / Rrim(I) all: 0.252 / Χ2: 1.02 / Net I/σ(I): 12.6
Reflection shellResolution: 2.6→2.85 Å / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 1.199 / Num. measured all: 74063 / Num. unique obs: 5238 / CC1/2: 0.824 / Rpim(I) all: 0.329 / Rrim(I) all: 1.244 / Χ2: 0.96 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→59.92 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 6815 5 %
Rwork0.1754 --
obs0.1786 136211 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→59.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28470 0 434 1133 30037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00929382
X-RAY DIFFRACTIONf_angle_d1.01239904
X-RAY DIFFRACTIONf_dihedral_angle_d18.32411118
X-RAY DIFFRACTIONf_chiral_restr0.0524730
X-RAY DIFFRACTIONf_plane_restr0.0075116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.31732530.2494244X-RAY DIFFRACTION100
2.63-2.660.32472260.23734258X-RAY DIFFRACTION100
2.66-2.690.33042110.2464335X-RAY DIFFRACTION100
2.69-2.730.31671940.23814214X-RAY DIFFRACTION100
2.73-2.760.30062150.22824317X-RAY DIFFRACTION100
2.76-2.80.32172260.22094265X-RAY DIFFRACTION100
2.8-2.840.30812190.22854253X-RAY DIFFRACTION100
2.84-2.880.28972500.22934287X-RAY DIFFRACTION100
2.88-2.930.29632200.22174238X-RAY DIFFRACTION100
2.93-2.980.31552320.23544304X-RAY DIFFRACTION100
2.98-3.030.32272000.22584246X-RAY DIFFRACTION100
3.03-3.080.32242360.21734321X-RAY DIFFRACTION100
3.08-3.140.29332300.20924255X-RAY DIFFRACTION100
3.14-3.210.30322180.20494321X-RAY DIFFRACTION100
3.21-3.280.28872070.20414253X-RAY DIFFRACTION100
3.28-3.350.26532260.2074335X-RAY DIFFRACTION100
3.35-3.440.28532340.21014250X-RAY DIFFRACTION100
3.44-3.530.29932170.20474323X-RAY DIFFRACTION100
3.53-3.630.26982340.1924318X-RAY DIFFRACTION100
3.63-3.750.27382150.1874277X-RAY DIFFRACTION100
3.75-3.880.25662080.1754314X-RAY DIFFRACTION100
3.88-4.040.22222190.15724349X-RAY DIFFRACTION100
4.04-4.220.1752250.13964323X-RAY DIFFRACTION100
4.22-4.450.1812430.13224339X-RAY DIFFRACTION100
4.45-4.720.18622300.1314321X-RAY DIFFRACTION100
4.72-5.090.19422390.13454343X-RAY DIFFRACTION100
5.09-5.60.21932320.14834400X-RAY DIFFRACTION100
5.6-6.410.18662330.15184406X-RAY DIFFRACTION100
6.41-8.070.18672820.13474392X-RAY DIFFRACTION100
8.07-59.920.1792410.13944595X-RAY DIFFRACTION99

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