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- PDB-7rk5: Mannitol-2-dehydrogenase bound to NADH from Aspergillus fumigatus -

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Basic information

Entry
Database: PDB / ID: 7rk5
TitleMannitol-2-dehydrogenase bound to NADH 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Mannitol 2-dehydrogenase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,3634
Polymers115,0332
Non-polymers1,3312
Water10,737596
1
B: Mannitol 2-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1822
Polymers57,5161
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Mannitol 2-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1822
Polymers57,5161
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)209.883, 71.289, 69.157
Angle α, β, γ (deg.)90.000, 101.150, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-779-

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: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 4000, 0.25 M lithium sulphate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.1→45.464 Å / Num. obs: 58465 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.069 / Rrim(I) all: 0.178 / Net I/σ(I): 8.6
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
2.1-2.166.71.8063012745190.5350.7471.9571.899.9
9.15-45.466.50.09548587480.990.0390.10318.798.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.44 Å45.46 Å
Translation5.44 Å45.46 Å

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RK4

7rk4


Resolution: 2.1→45.46 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 2886 4.94 %
Rwork0.1898 55569 -
obs0.1927 58455 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.16 Å2 / Biso mean: 37.7683 Å2 / Biso min: 17.02 Å2
Refinement stepCycle: final / Resolution: 2.1→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7656 0 88 596 8340
Biso mean--39.08 41.54 -
Num. residues----990
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.13440.41421440.32142613100
2.1344-2.17120.31261390.27562658100
2.1712-2.21070.3291420.26222604100
2.2107-2.25320.31611450.24932613100
2.2532-2.29920.28871380.24442657100
2.2992-2.34920.34381490.24322592100
2.3492-2.40390.30311450.24263199
2.4039-2.4640.30241340.2298265499
2.464-2.53060.26591170.2092620100
2.5306-2.60510.29481300.20282651100
2.6051-2.68910.26521250.1979263299
2.6891-2.78520.25881440.20342645100
2.7852-2.89670.27151300.20342637100
2.8967-3.02850.28571250.19882636100
3.0285-3.18820.25641290.20132687100
3.1882-3.38790.2641340.18522660100
3.3879-3.64930.23411560.17072642100
3.6493-4.01640.21691540.15232651100
4.0164-4.59710.16841440.1402264799
4.5971-5.790.18881290.16572683100
5.79-45.460.2471330.17872756100

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