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- PDB-9ffk: Vanillyl alcohol oxidase from Novosphingobium sp in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9ffk
TitleVanillyl alcohol oxidase from Novosphingobium sp in complex with vanillyl alcohol
ComponentsFAD-binding oxidoreductase
KeywordsHYDROLASE / FAD / flavin / hydroxylase / alcohol / enzyme mechanism
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 / 4-hydroxy-3-methoxybenzaldehyde / FAD-binding oxidoreductase
Similarity search - Component
Biological speciesNovosphingobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)112,5409
Polymers110,3882
Non-polymers2,1527
Water10,052558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-60 kcal/mol
Surface area32040 Å2
Unit cell
Length a, b, c (Å)90.845, 96.766, 129.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein FAD-binding oxidoreductase


Mass: 55194.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium sp. (bacteria) / Gene: EH199_11270 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3N9RU39
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Morpheus H2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.7→129.11 Å / Num. obs: 125029 / % possible obs: 99.7 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.037 / Rrim(I) all: 0.167 / Χ2: 1.01 / Net I/σ(I): 10.1 / Num. measured all: 2499402
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 99.7 % / Redundancy: 18.6 % / Rmerge(I) obs: 2.466 / Num. measured all: 113543 / Num. unique obs: 6098 / CC1/2: 0.707 / Rpim(I) all: 0.584 / Rrim(I) all: 2.535 / Χ2: 0.91 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→90.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.86 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2535 6198 5 %RANDOM
Rwork0.22274 ---
obs0.22426 118543 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0 Å2
2---1.62 Å20 Å2
3---1.76 Å2
Refinement stepCycle: 1 / Resolution: 1.7→90.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7758 0 146 558 8462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138117
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177567
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.64511047
X-RAY DIFFRACTIONr_angle_other_deg1.4491.57517408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07251000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69422.101395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56151273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2861548
X-RAY DIFFRACTIONr_chiral_restr0.090.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029220
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021870
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_it2.3292.4644006
X-RAY DIFFRACTIONr_mcbond_other2.3292.4634005
X-RAY DIFFRACTIONr_mcangle_it3.253.6925004
X-RAY DIFFRACTIONr_mcangle_other3.253.6925005
X-RAY DIFFRACTIONr_scbond_it3.2122.7894111
X-RAY DIFFRACTIONr_scbond_other3.2122.7884112
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6934.0576044
X-RAY DIFFRACTIONr_long_range_B_refined6.02729.5289330
X-RAY DIFFRACTIONr_long_range_B_other629.3579254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 444 -
Rwork0.35 8677 -
obs--99.76 %

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