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- PDB-7rk4: Mannitol-2-dehydrogenase from Aspergillus fumigatus -

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Basic information

Entry
Database: PDB / ID: 7rk4
TitleMannitol-2-dehydrogenase from Aspergillus fumigatus
ComponentsMannitol 2-dehydrogenase
KeywordsOXIDOREDUCTASE / mannitol biosynthesis
Function / homology
Function and homology information


mannitol dehydrogenase activity / mannitol 2-dehydrogenase / mannitol 2-dehydrogenase activity / mannitol metabolic process / NAD binding / NADP binding
Similarity search - Function
: / Mannitol dehydrogenase / Mannitol dehydrogenase, N-terminal / Mannitol dehydrogenase Rossmann domain / Mannitol dehydrogenase, C-terminal / Mannitol dehydrogenase C-terminal domain / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Mannitol 2-dehydrogenase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsNguyen, S. / Bruning, J.B.
CitationJournal: To Be Published
Title: Targeting the Mannitol Biosynthesis Pathway in Aspergillus fumigatus: Characterisation and Inhibition of Mannitol-2-Dehydrogenase
Authors: Nguyen, S. / Jovcevski, B. / Pukala, T.L. / Bruning, J.B.
History
DepositionJul 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannitol 2-dehydrogenase
B: Mannitol 2-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)115,0332
Polymers115,0332
Non-polymers00
Water27,3831520
1
A: Mannitol 2-dehydrogenase


  • defined by author&software
  • Evidence: mass spectrometry, Native mass spectrometry indicates that mannitol-2-dehydrogenase forms a dimer in the gas phase, gel filtration, Gel filtration experiments indicate that mannitol-2- ...Evidence: mass spectrometry, Native mass spectrometry indicates that mannitol-2-dehydrogenase forms a dimer in the gas phase, gel filtration, Gel filtration experiments indicate that mannitol-2-dehydrogenase is dimeric in the solution phase
  • 57.5 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)57,5161
Polymers57,5161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mannitol 2-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)57,5161
Polymers57,5161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)219.483, 75.036, 69.648
Angle α, β, γ (deg.)90.000, 106.260, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1335-

HOH

21B-901-

HOH

31B-956-

HOH

41B-1346-

HOH

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Components

#1: Protein Mannitol 2-dehydrogenase / M2DH / MDH


Mass: 57516.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_4G14450 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4WQY4, mannitol 2-dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1520 / Source method: isolated from a natural source / Formula: H2O

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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: 48.6 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3350, 0.15 M Tris pH 8.5, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.7→46.43 Å / Num. obs: 117244 / % possible obs: 98.4 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.037 / Rrim(I) all: 0.1 / Net I/σ(I): 12.4 / Num. measured all: 831426 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.7372.1593980056510.440.8652.329196.2
9.31-46.437.10.02454537700.9980.010.02654.298.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.7 Å45.41 Å
Translation1.7 Å45.41 Å

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ILJ8

Resolution: 1.8→45.418 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 5268 5.32 %
Rwork0.1645 93808 -
obs0.1667 99076 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.29 Å2 / Biso mean: 29.7322 Å2 / Biso min: 12.14 Å2
Refinement stepCycle: final / Resolution: 1.8→45.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7829 0 0 1520 9349
Biso mean---40.62 -
Num. residues----1004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82050.33071680.2806306197
1.8205-1.84190.2981620.2646307498
1.8419-1.86430.29721700.2517310097
1.8643-1.88790.25781790.2425306898
1.8879-1.91280.32471840.2314306798
1.9128-1.9390.26071590.2332312898
1.939-1.96670.27961820.218306398
1.9667-1.9960.23831860.2092310398
1.996-2.02720.25551620.1929310298
2.0272-2.06050.24651940.1948305498
2.0605-2.0960.24951690.1898313398
2.096-2.13410.25271620.1872310098
2.1341-2.17520.24491530.1774316098
2.1752-2.21960.21311690.176309498
2.2196-2.26780.24451730.1806314398
2.2678-2.32060.21391560.1721314699
2.3206-2.37860.23431910.1675305898
2.3786-2.44290.19211860.1704313399
2.4429-2.51480.24631880.1679316099
2.5148-2.5960.23241830.1696310699
2.596-2.68870.22711530.1688318899
2.6887-2.79640.21741850.1742311499
2.7964-2.92360.2461710.1702314899
2.9236-3.07770.20711820.1702314299
3.0777-3.27050.22021820.162317399
3.2705-3.52290.17721560.1479320099
3.5229-3.87730.15811670.1384318599
3.8773-4.43790.13561820.1223316499
4.4379-5.58970.16622240.1324315999
5.5897-45.4180.1851900.15513282100

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