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- PDB-8s7u: Vanillyl-alcohol dehydrogenase from Marinicaulis flavus: P151L mutant -

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Basic information

Entry
Database: PDB / ID: 8s7u
TitleVanillyl-alcohol dehydrogenase from Marinicaulis flavus: P151L mutant
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / FAD / flavin / 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
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)119,72025
Polymers116,5242
Non-polymers3,19623
Water12,935718
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14190 Å2
ΔGint-93 kcal/mol
Surface area32750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.495, 138.495, 180.947
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) / References: UniProt: A0A2S7K3M2

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Non-polymers , 5 types, 741 molecules

#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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / 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: 3.72 Å3/Da / Density % sol: 66.96 %
Crystal growTemperature: 293 K / Method: evaporation
Details: Condition C4 of Morpheus screening from 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→48.97 Å / Num. obs: 161652 / % possible obs: 99.7 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.041 / Rrim(I) all: 0.152 / Χ2: 1 / Net I/σ(I): 11.8 / Num. measured all: 2179134
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 2.885 / Num. measured all: 106435 / Num. unique obs: 7961 / CC1/2: 0.39 / Rpim(I) all: 0.816 / Rrim(I) all: 3 / Χ2: 0.94 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.31 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.287 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18005 8004 5 %RANDOM
Rwork0.15466 ---
obs0.1559 153545 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.464 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.65 Å2-0 Å2
3----1.31 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8180 0 208 718 9106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0138601
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177832
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.64611694
X-RAY DIFFRACTIONr_angle_other_deg1.4971.57818050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97251035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62322.162444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.955151321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5841552
X-RAY DIFFRACTIONr_chiral_restr0.0930.21061
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.029735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021977
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_it2.3012.7394146
X-RAY DIFFRACTIONr_mcbond_other2.3012.7394145
X-RAY DIFFRACTIONr_mcangle_it2.8294.0955179
X-RAY DIFFRACTIONr_mcangle_other2.8284.0955180
X-RAY DIFFRACTIONr_scbond_it4.0773.1544455
X-RAY DIFFRACTIONr_scbond_other4.0713.1484443
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5364.5496501
X-RAY DIFFRACTIONr_long_range_B_refined6.43932.92510034
X-RAY DIFFRACTIONr_long_range_B_other6.40732.5619862
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
Rfree0.328 597 -
Rwork0.322 11259 -
obs--100 %

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