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- PDB-8s7r: Vanillyl-alcohol dehydrogenase from Marinicaulis flavus: P151T mutant -

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Basic information

Entry
Database: PDB / ID: 8s7r
TitleVanillyl-alcohol dehydrogenase from Marinicaulis flavus: P151T 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 / DI(HYDROXYETHYL)ETHER / Oxidoreductase
Similarity search - Component
Biological speciesMarinicaulis flavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)177,50210
Polymers174,7493
Non-polymers2,7537
Water8,431468
1
A: Oxidoreductase
hetero molecules

A: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,4678
Polymers116,5002
Non-polymers1,9686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area11010 Å2
ΔGint-76 kcal/mol
Surface area34510 Å2
MethodPISA
2
B: Oxidoreductase
C: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2696
Polymers116,5002
Non-polymers1,7694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10380 Å2
ΔGint-82 kcal/mol
Surface area34530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.949, 144.451, 286.785
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
11A-794-

HOH

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Components

#1: Protein Oxidoreductase


Mass: 58249.785 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) / References: UniProt: A0A2S7K3M2
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5 / Details: 0.2 M NaCl 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-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.9→286.79 Å / Num. obs: 146187 / % possible obs: 97.8 % / Redundancy: 3.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.038 / Rrim(I) all: 0.077 / Χ2: 1.03 / Net I/σ(I): 9.2 / Num. measured all: 545266
Reflection shellResolution: 1.9→1.93 Å / % possible obs: 98.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 1.253 / Num. measured all: 27438 / Num. unique obs: 7204 / CC1/2: 0.423 / Rpim(I) all: 0.724 / Rrim(I) all: 1.457 / Χ2: 1.04 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→143.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.178 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23456 7243 5 %RANDOM
Rwork0.19374 ---
obs0.1958 138852 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.549 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å20 Å2-0 Å2
2---0.58 Å2-0 Å2
3----2.22 Å2
Refinement stepCycle: 1 / Resolution: 1.9→143.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12236 0 185 468 12889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01212778
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611671
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.65117419
X-RAY DIFFRACTIONr_angle_other_deg0.4561.56826898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22351551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.921578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.889101971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.21832
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214930
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022956
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_it3.5194.4496213
X-RAY DIFFRACTIONr_mcbond_other3.5194.4496213
X-RAY DIFFRACTIONr_mcangle_it4.7317.9917761
X-RAY DIFFRACTIONr_mcangle_other4.7317.9917762
X-RAY DIFFRACTIONr_scbond_it4.1044.8176565
X-RAY DIFFRACTIONr_scbond_other4.1034.8186566
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0258.6949659
X-RAY DIFFRACTIONr_long_range_B_refined10.14945.9114886
X-RAY DIFFRACTIONr_long_range_B_other9.48845.2514809
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 515 -
Rwork0.352 10260 -
obs--98.18 %

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