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- PDB-8bam: Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, tenfold muta... -

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Basic information

Entry
Database: PDB / ID: 8bam
TitleEugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, tenfold mutant active on propanol syringol
ComponentsProbable vanillyl-alcohol oxidase
KeywordsOXIDOREDUCTASE / Biocatalysis / lignin / FAD / flavoenzyme
Function / homology
Function and homology information


vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / D-lactate dehydrogenase activity / FAD binding / metal ion binding
Similarity search - Function
Cytokinin dehydrogenase, C-terminal domain superfamily / FAD-linked oxidase, C-terminal / 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. ...Cytokinin dehydrogenase, C-terminal domain superfamily / FAD-linked oxidase, C-terminal / 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 / 2,6-dimethoxy-4-(3-oxidanylpropyl)phenol / Probable vanillyl-alcohol oxidase
Similarity search - Component
Biological speciesRhodococcus jostii RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAlvigini, L. / Mattevi, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)Grant Agreement No. 837890 (SMARTBOX).European Union
CitationJournal: Acs Catalysis / Year: 2023
Title: One-Pot Biocatalytic Synthesis of rac -Syringaresinol from a Lignin-Derived Phenol.
Authors: Guo, Y. / Alvigini, L. / Saifuddin, M. / Ashley, B. / Trajkovic, M. / Alonso-Cotchico, L. / Mattevi, A. / Fraaije, M.W.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_validate_close_contact / struct_conn
Item: _citation.pdbx_database_id_DOI / _citation_author.name
Revision 1.2Dec 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9258
Polymers117,7452
Non-polymers2,1806
Water12,665703
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-73 kcal/mol
Surface area33610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.654, 98.058, 177.336
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Probable vanillyl-alcohol oxidase


Mass: 58872.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Strain: RHA1 / 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-QBF / 2,6-dimethoxy-4-(3-oxidanylpropyl)phenol / propanol syringol


Mass: 212.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M TrizmaHCl pH 8.0, 25% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.65→49.7 Å / Num. obs: 120308 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.023 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5385 / CC1/2: 0.609 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3546refinement
PHENIX1.16_3546refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FXD

5fxd


Resolution: 1.65→49.7 Å / SU ML: 0.1662 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8416
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206 6038 5.02 %
Rwork0.1724 114136 -
obs0.1741 120174 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.43 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8266 0 148 703 9117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00698640
X-RAY DIFFRACTIONf_angle_d0.944711740
X-RAY DIFFRACTIONf_chiral_restr0.05281212
X-RAY DIFFRACTIONf_plane_restr0.00621542
X-RAY DIFFRACTIONf_dihedral_angle_d4.8165058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.30341810.2833282X-RAY DIFFRACTION86.75
1.67-1.690.28891900.26133795X-RAY DIFFRACTION99.8
1.69-1.710.28242040.23843728X-RAY DIFFRACTION99.95
1.71-1.730.27432330.23033760X-RAY DIFFRACTION99.92
1.73-1.760.25542210.22473773X-RAY DIFFRACTION99.87
1.76-1.780.2621680.2253807X-RAY DIFFRACTION99.9
1.78-1.810.25981970.21393823X-RAY DIFFRACTION99.85
1.81-1.830.27192130.20563713X-RAY DIFFRACTION99.85
1.83-1.860.24452050.21033836X-RAY DIFFRACTION99.83
1.86-1.890.22992080.20363752X-RAY DIFFRACTION99.87
1.89-1.930.22262130.18543790X-RAY DIFFRACTION99.98
1.93-1.960.21231960.18373791X-RAY DIFFRACTION100
1.96-20.20182130.17563763X-RAY DIFFRACTION99.9
2-2.040.21331900.16743802X-RAY DIFFRACTION99.95
2.04-2.080.211940.173814X-RAY DIFFRACTION99.93
2.08-2.130.22342210.17463812X-RAY DIFFRACTION99.93
2.13-2.180.20551910.17013782X-RAY DIFFRACTION99.82
2.18-2.240.23172090.17053785X-RAY DIFFRACTION99.87
2.24-2.310.23341990.16863835X-RAY DIFFRACTION99.88
2.31-2.380.21211960.17643819X-RAY DIFFRACTION99.93
2.38-2.470.21561760.17793829X-RAY DIFFRACTION99.93
2.47-2.570.22091890.17313839X-RAY DIFFRACTION99.88
2.57-2.690.191830.16693838X-RAY DIFFRACTION99.83
2.69-2.830.21922180.16593828X-RAY DIFFRACTION99.8
2.83-30.18622020.16883855X-RAY DIFFRACTION99.8
3-3.240.22052000.16773868X-RAY DIFFRACTION99.73
3.24-3.560.16812080.15043846X-RAY DIFFRACTION99.27
3.56-4.080.17481930.1483919X-RAY DIFFRACTION99.95
4.08-5.140.17242180.14723932X-RAY DIFFRACTION99.78
5.14-490.17662090.1734120X-RAY DIFFRACTION99.61

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