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- PDB-9jaw: Crystal structure of NAD-dependent methanol dehydrogenases 2 from... -

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Basic information

Entry
Database: PDB / ID: 9jaw
TitleCrystal structure of NAD-dependent methanol dehydrogenases 2 from Bacillus methanolicus MGA3
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
: / NAD-dependent methanol dehydrogenase
Similarity search - Component
Biological speciesBacillus methanolicus MGA3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 dehydrogenases 2 from Bacillus methanolicus MGA3
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)418,69021
Polymers418,11810
Non-polymers57211
Water55831
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)83.330, 203.530, 254.940
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate, 0.1 M Bis Tris propane, pH 7.0, 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: 2.5→39.6 Å / Num. obs: 150533 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.309 / Rpim(I) all: 0.086 / Rrim(I) all: 0.321 / Χ2: 1 / Net I/σ(I): 9.8 / Num. measured all: 2047251
Reflection shellResolution: 2.5→2.56 Å / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 1.992 / Num. measured all: 153541 / Num. unique obs: 11001 / CC1/2: 0.557 / Rpim(I) all: 0.55 / Rrim(I) all: 2.067 / Χ2: 0.95 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.21 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 5441 5.06 %
Rwork0.2002 --
obs0.2026 107487 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28470 0 11 31 28512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00828920
X-RAY DIFFRACTIONf_angle_d1.37739200
X-RAY DIFFRACTIONf_dihedral_angle_d17.41210580
X-RAY DIFFRACTIONf_chiral_restr0.0784650
X-RAY DIFFRACTIONf_plane_restr0.0145090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.34821820.2893354X-RAY DIFFRACTION100
2.83-2.870.33711940.26443383X-RAY DIFFRACTION100
2.87-2.90.32511460.25773368X-RAY DIFFRACTION100
2.9-2.940.3241630.24713354X-RAY DIFFRACTION100
2.94-2.980.33071990.25423389X-RAY DIFFRACTION100
2.98-3.020.31661740.2483328X-RAY DIFFRACTION100
3.02-3.060.31391630.26863398X-RAY DIFFRACTION100
3.06-3.10.33551930.26063370X-RAY DIFFRACTION100
3.1-3.150.28551700.26123339X-RAY DIFFRACTION100
3.15-3.210.30921810.25183423X-RAY DIFFRACTION100
3.21-3.260.33982010.2473300X-RAY DIFFRACTION100
3.26-3.320.2961690.24113398X-RAY DIFFRACTION100
3.32-3.380.28811950.23753359X-RAY DIFFRACTION100
3.38-3.450.281960.22263366X-RAY DIFFRACTION100
3.45-3.530.2751670.22313362X-RAY DIFFRACTION100
3.53-3.610.22961960.21363398X-RAY DIFFRACTION100
3.61-3.70.261860.2123373X-RAY DIFFRACTION100
3.7-3.80.27641910.213390X-RAY DIFFRACTION100
3.8-3.910.23251640.19653394X-RAY DIFFRACTION100
3.91-4.040.2161960.17983373X-RAY DIFFRACTION100
4.04-4.180.20411620.16933433X-RAY DIFFRACTION100
4.18-4.350.22731630.16483425X-RAY DIFFRACTION100
4.35-4.550.19391860.16213406X-RAY DIFFRACTION100
4.55-4.790.19381920.16243413X-RAY DIFFRACTION100
4.79-5.080.2161740.1683432X-RAY DIFFRACTION100
5.08-5.480.24791760.19273451X-RAY DIFFRACTION100
5.48-6.030.2331760.1943463X-RAY DIFFRACTION100
6.03-6.890.22341920.18573471X-RAY DIFFRACTION100
6.89-8.670.17941910.14983505X-RAY DIFFRACTION100
8.67-39.210.17322030.14883628X-RAY DIFFRACTION99

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