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- PDB-9fge: Vanillyl alcohol oxidase from Novosphingobium sp: T181D mutant in... -

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Basic information

Entry
Database: PDB / ID: 9fge
TitleVanillyl alcohol oxidase from Novosphingobium sp: T181D mutant in complex with vanillin
ComponentsFAD-binding oxidoreductase
KeywordsFLAVOPROTEIN / FAD / flavin / hydroxylase / alcohol / enzyme
Function / homology
Function and homology information


lactate catabolic process / D-lactate dehydrogenase (cytochrome) activity / D-lactate dehydrogenase (NAD+) activity / FAD binding
Similarity search - Function
FAD-linked oxidase, C-terminal / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. ...FAD-linked oxidase, C-terminal / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / 4-hydroxy-3-methoxybenzaldehyde / FAD-binding oxidoreductase
Similarity search - Component
Biological speciesNovosphingobium sp. 01WB02.4-10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGuerriere, T.B. / Mattevi, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2025
Title: Dehydrogenase versus oxidase function: the interplay between substrate binding and flavin microenvironment.
Authors: Guerriere, T.B. / Vancheri, A. / Ricotti, I. / Serapian, S.A. / Eggerichs, D. / Tischler, D. / Colombo, G. / Mascotti, M.L. / Fraaije, M.W. / Mattevi, A.
History
DepositionMay 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 5, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD-binding oxidoreductase
B: FAD-binding oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5829
Polymers110,4162
Non-polymers2,1667
Water13,908772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10950 Å2
ΔGint-53 kcal/mol
Surface area32120 Å2
Unit cell
Length a, b, c (Å)91.326, 97.824, 129.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-1081-

HOH

21B-1091-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FAD-binding oxidoreductase


Mass: 55207.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium sp. 01WB02.4-10 (bacteria)
Gene: EH199_11270 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3N9RU39

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Non-polymers , 5 types, 779 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-V55 / 4-hydroxy-3-methoxybenzaldehyde / p-vanillin


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 772 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 293.5 K / Method: evaporation / pH: 6.5 / Details: PEG 20000 15%, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.6→78.2 Å / Num. obs: 152440 / % possible obs: 99.6 % / Redundancy: 9.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.051 / Rrim(I) all: 0.158 / Χ2: 1.02 / Net I/σ(I): 8.8
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 99.3 % / Redundancy: 9.1 % / Rmerge(I) obs: 1.476 / Num. measured all: 67952 / Num. unique obs: 7444 / CC1/2: 0.793 / Rpim(I) all: 0.504 / Rrim(I) all: 1.562 / Χ2: 1.01 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→78.2 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.633 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20382 7529 4.9 %RANDOM
Rwork0.17512 ---
obs0.1765 144823 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.011 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-0 Å2
2--0.74 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.6→78.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7740 0 147 772 8659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0128100
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167533
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.64911023
X-RAY DIFFRACTIONr_angle_other_deg0.5791.56617323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86751000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.739552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.274101262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.21172
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029476
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021874
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7371.5374006
X-RAY DIFFRACTIONr_mcbond_other1.7371.5374006
X-RAY DIFFRACTIONr_mcangle_it2.5592.7635004
X-RAY DIFFRACTIONr_mcangle_other2.5592.7635005
X-RAY DIFFRACTIONr_scbond_it3.0531.7934094
X-RAY DIFFRACTIONr_scbond_other3.0531.7944095
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5743.1516020
X-RAY DIFFRACTIONr_long_range_B_refined5.6816.59519
X-RAY DIFFRACTIONr_long_range_B_other5.58515.229328
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 541 -
Rwork0.29 10574 -
obs--99.24 %

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