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- PDB-7wmd: PQQ-dependent alcohol dehydrogenase detoxifying DON -

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Basic information

Entry
Database: PDB / ID: 7wmd
TitlePQQ-dependent alcohol dehydrogenase detoxifying DON
ComponentsPQQ-dependent alcohol dehydrogenase
KeywordsTOXIN / Dehydrogenase / PQQ
Function / homologyQuinoprotein alcohol dehydrogenase-like superfamily / 8 Propeller / Methanol Dehydrogenase; Chain A / Mainly Beta
Function and homology information
Biological speciesDevosia albogilva (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, M. / Yang, H. / Lv, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000889 China
CitationJournal: J.Agric.Food Chem. / Year: 2022
Title: Structure-Function Analysis of a Quinone-Dependent Dehydrogenase Capable of Deoxynivalenol Detoxification.
Authors: Yang, H. / Yan, R. / Li, Y. / Lu, Z. / Bie, X. / Zhao, H. / Lu, F. / Chen, M.
History
DepositionJan 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PQQ-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0294
Polymers61,9081
Non-polymers1203
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-10 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.539, 90.536, 57.294
Angle α, β, γ (deg.)90.000, 103.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-823-

HOH

21A-998-

HOH

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Components

#1: Protein PQQ-dependent alcohol dehydrogenase


Mass: 61908.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Devosia albogilva (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2M Magnesium chloride hexahydrate, 0.1M BIS-Tris pH 5.5, 25% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→40.43 Å / Num. obs: 37502 / % possible obs: 99 % / Redundancy: 6.63 % / CC1/2: 0.997 / Net I/σ(I): 15.33
Reflection shellResolution: 2→2.071 Å / Mean I/σ(I) obs: 5.41 / Num. unique obs: 5902 / CC1/2: 0.942 / % possible all: 97

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CVB

4cvb


Resolution: 2→40.43 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 2000 5.44 %
Rwork0.1678 34798 -
obs0.1705 36798 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.99 Å2 / Biso mean: 21.8135 Å2 / Biso min: 0.31 Å2
Refinement stepCycle: final / Resolution: 2→40.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 3 336 4344
Biso mean--9.15 27.13 -
Num. residues----531
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.24541410.17542464260599
2.05-2.110.2381420.17952466260899
2.11-2.170.24491410.17092457259899
2.17-2.240.24251430.16422477262099
2.24-2.320.24311430.17432478262199
2.32-2.410.20341400.16262436257699
2.41-2.520.22911430.17062494263799
2.52-2.650.2561430.174424892632100
2.65-2.820.2341410.17862473261499
2.82-3.040.23811440.17372484262899
3.04-3.340.22111440.174825132657100
3.34-3.820.21071440.156725012645100
3.83-4.820.16281450.134325162661100
4.82-40.430.21081460.192225502696100

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