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- PDB-9gj0: Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, mutant B1 -

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Basic information

Entry
Database: PDB / ID: 9gj0
TitleEugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, mutant B1
ComponentsProbable vanillyl-alcohol oxidase
KeywordsOXIDOREDUCTASE / Mutant / vanillyl alcohol oxidase / ether cleavage
Function / homology
Function and homology information


vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / D-lactate dehydrogenase (NAD+) activity / FAD binding / metal ion 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 / Probable vanillyl-alcohol oxidase
Similarity search - Component
Biological speciesRhodococcus jostii RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2025
Title: Biocatalytic Cleavage of para-Acetoxy Benzyl Ethers: Application to Protecting Group Chemistry
Authors: Ashley, B. / Demingo, C. / Rozeboom, H. / Bianciardi, N. / Dunleavy, T. / Haaksma, J.J. / Guo, Y. / Fraaije, M.W.
History
DepositionAug 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable vanillyl-alcohol oxidase
B: Probable vanillyl-alcohol oxidase
C: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,8235
Polymers185,2523
Non-polymers1,5712
Water00
1
A: Probable vanillyl-alcohol oxidase
hetero molecules

A: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,0724
Polymers123,5012
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area10000 Å2
ΔGint-75 kcal/mol
Surface area33830 Å2
MethodPISA
2
B: Probable vanillyl-alcohol oxidase
C: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2873
Polymers123,5012
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-66 kcal/mol
Surface area34470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.770, 109.770, 244.985
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Probable vanillyl-alcohol oxidase


Mass: 61750.688 Da / Num. of mol.: 3
Mutation: S81H, R378Q, D283H, E378D, S394V, A423M, Q425G, I427T, H434Y, I445D, S518P, +GKLGPEQKLISEEDLNSAVDHHHHHH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Gene: RHA1_ro03282 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0SBK1, vanillyl-alcohol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
Has ligand of interestN
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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium Sulphate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.76→244.99 Å / Num. obs: 43581 / % possible obs: 97 % / Redundancy: 19.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.03 / Rrim(I) all: 0.131 / Χ2: 1.02 / Net I/σ(I): 18.4 / Num. measured all: 836685
Reflection shellResolution: 2.76→2.86 Å / % possible obs: 100 % / Redundancy: 17.9 % / Rmerge(I) obs: 3.475 / Num. measured all: 83399 / Num. unique obs: 4650 / CC1/2: 0.389 / Rpim(I) all: 0.839 / Rrim(I) all: 3.576 / Χ2: 0.86 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→95.06 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 20.978 / SU ML: 0.391 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26558 2181 5 %RANDOM
Rwork0.20591 ---
obs0.20898 41342 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.651 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å2-0 Å2
2---0.54 Å20 Å2
3---1.77 Å2
Refinement stepCycle: 1 / Resolution: 2.76→95.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12256 0 106 0 12362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01212699
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611691
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.82817259
X-RAY DIFFRACTIONr_angle_other_deg0.5051.75226952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77651555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.957583
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.631102022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.21797
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215227
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022965
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_it8.9969.8236232
X-RAY DIFFRACTIONr_mcbond_other8.9959.8236232
X-RAY DIFFRACTIONr_mcangle_it12.83717.6617783
X-RAY DIFFRACTIONr_mcangle_other12.83617.6617784
X-RAY DIFFRACTIONr_scbond_it8.85710.4036467
X-RAY DIFFRACTIONr_scbond_other8.85610.4046468
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.13118.9059477
X-RAY DIFFRACTIONr_long_range_B_refined16.53494.3314049
X-RAY DIFFRACTIONr_long_range_B_other16.53494.3314050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.76→2.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 145 -
Rwork0.349 3123 -
obs--100 %

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