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- PDB-8s7n: Vanillyl-alcohol dehydrogenase from Marinicaulis flavus: P151L mu... -

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Basic information

Entry
Database: PDB / ID: 8s7n
TitleVanillyl-alcohol dehydrogenase from Marinicaulis flavus: P151L mutant bound to eugenol
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / FAD / flavim oxidase / 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
Similarity search - Domain/homology
2-methoxy-4-(prop-2-en-1-yl)phenol / FLAVIN-ADENINE DINUCLEOTIDE / NITRATE ION / DI(HYDROXYETHYL)ETHER / Oxidoreductase
Similarity search - Component
Biological speciesMarinicaulis flavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGuerriere, T.B. / Mattevi, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionB-Ligzymes (GA 824017)European Union
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
DepositionMar 4, 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

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,06920
Polymers116,5242
Non-polymers3,54518
Water16,520917
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13610 Å2
ΔGint-53 kcal/mol
Surface area33030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.019, 139.019, 181.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Oxidoreductase


Mass: 58261.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinicaulis flavus (bacteria) / Gene: CW354_13745 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB10beta / References: UniProt: A0A2S7K3M2

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Non-polymers , 7 types, 935 molecules

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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#7: Chemical ChemComp-EOL / 2-methoxy-4-(prop-2-en-1-yl)phenol / eugenol


Mass: 164.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 917 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.75 Å3/Da / Density % sol: 67.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: Condition C4 of the Morpheus screen (Hampton research)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.8→49.2 Å / Num. obs: 163464 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.054 / Rrim(I) all: 0.201 / Χ2: 1 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 3.735 / Num. measured all: 107003 / Num. unique obs: 8025 / CC1/2: 0.388 / Rpim(I) all: 1.051 / Rrim(I) all: 3.882 / Χ2: 0.97 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.9data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.2 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.382 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18397 8262 5.1 %RANDOM
Rwork0.15754 ---
obs0.15887 155094 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.553 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å2-0 Å2-0 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refinement stepCycle: 1 / Resolution: 1.8→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8174 0 239 917 9330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0138641
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177910
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.64611735
X-RAY DIFFRACTIONr_angle_other_deg1.4851.57718228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11151036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60722.162444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.075151318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4991552
X-RAY DIFFRACTIONr_chiral_restr0.0930.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029750
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021990
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_it2.0472.424150
X-RAY DIFFRACTIONr_mcbond_other2.0472.4194149
X-RAY DIFFRACTIONr_mcangle_it2.6573.6185184
X-RAY DIFFRACTIONr_mcangle_other2.6563.6195185
X-RAY DIFFRACTIONr_scbond_it3.482.8054491
X-RAY DIFFRACTIONr_scbond_other3.4792.8054492
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9814.056552
X-RAY DIFFRACTIONr_long_range_B_refined6.06129.81910256
X-RAY DIFFRACTIONr_long_range_B_other5.96629.24610018
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 599 -
Rwork0.327 11336 -
obs--100 %

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