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- PDB-8s7p: Vanillyl-alcohol dehydrogenase from Marinicaulis flavus -

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Basic information

Entry
Database: PDB / ID: 8s7p
TitleVanillyl-alcohol dehydrogenase from Marinicaulis flavus
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / FAD / flavin / oxidase / alcohol / enzyme mechanism
Function / homology
Function and homology information


D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / 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
FLAVIN-ADENINE DINUCLEOTIDE / Oxidoreductase
Similarity search - Component
Biological speciesMarinicaulis flavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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
C: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,0946
Polymers174,7373
Non-polymers2,3573
Water86548
1
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0634
Polymers116,4922
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-84 kcal/mol
Surface area34330 Å2
MethodPISA
2
C: Oxidoreductase
hetero molecules

C: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0634
Polymers116,4922
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9940 Å2
ΔGint-85 kcal/mol
Surface area34140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.142, 143.224, 287.748
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-704-

HOH

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Components

#1: Protein Oxidoreductase


Mass: 58245.801 Da / Num. of mol.: 3
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
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.2 M Ammonium chloride and 20% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.35→67.49 Å / Num. obs: 77772 / % possible obs: 100 % / Redundancy: 21.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.037 / Rrim(I) all: 0.17 / Χ2: 0.92 / Net I/σ(I): 12.6
Reflection shellResolution: 2.35→2.4 Å / % possible obs: 99.6 % / Redundancy: 16.1 % / Rmerge(I) obs: 3.295 / Num. measured all: 72661 / Num. unique obs: 4521 / CC1/2: 0.488 / Rpim(I) all: 0.836 / Rrim(I) all: 3.403 / Χ2: 0.84 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→67.49 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.831 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27907 3964 5.1 %RANDOM
Rwork0.22789 ---
obs0.23056 73750 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.108 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å2-0 Å20 Å2
2--2.66 Å2-0 Å2
3----3.35 Å2
Refinement stepCycle: 1 / Resolution: 2.35→67.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12182 0 159 48 12389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01212703
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611575
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.65117332
X-RAY DIFFRACTIONr_angle_other_deg0.5181.56826659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.87851550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.376577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.366101938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.21826
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214878
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022949
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_it5.4085.5136209
X-RAY DIFFRACTIONr_mcbond_other5.4085.5136209
X-RAY DIFFRACTIONr_mcangle_it7.689.9167756
X-RAY DIFFRACTIONr_mcangle_other7.689.9167757
X-RAY DIFFRACTIONr_scbond_it5.7945.8666494
X-RAY DIFFRACTIONr_scbond_other5.7895.8666491
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.38610.6319577
X-RAY DIFFRACTIONr_long_range_B_refined10.87154.1114449
X-RAY DIFFRACTIONr_long_range_B_other10.87154.1114450
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.554 287 -
Rwork0.556 5360 -
obs--99.63 %

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